Applications
(Redirected from Installed Software)
Jump to navigation
Jump to search
Note: Up to three latest versions are listed even though there could be more available. Run module spider keyword
for a full list of provided versions. Use the Module value from the second column below as the keyword.
If it's a 'core' module you should be able to directly combine the Module name and a Version for a load command e.g. 'module load pylucene'.
Name | Module | Versions | URL | Categories
|
---|---|---|---|---|
3d-dna | 3d-dna | 20170330 | [1] | biology, phylogenetics |
3PCLR | 3pclr | 20150906 | [2] | biology, phylogenetics |
4p | 4p | 1.0 | [3] | biology, variant_calling |
AAFTF | aaftf | 0.2.5, 0.4.1 | [4] | biology, pipeline, assembly |
ABRicate | abricate | 1.0.1 | [5] | phylogenetics |
ABruijn | abruijn | 1.0 | [6] | biology, assembly, ngs |
ABySS | abyss | 2.1.0, 2.2.5, 2.3.7 | [7] | biology, de_novo |
ACTC | actc | 0.3.1 | [8] | biology |
AdapterRemoval | adapterremoval | 2.2.2 | [9] | phylogenetics |
ADFRsuite | adfrsuite | 1.0 | [10] | sequencing, biology |
ADMB | admb | 11.5, 12.0 | [11] | math, modeling |
AdmixTools | admixtools | 20150311, 7.0.2 | [12] | biology, genomics, ngs |
ADMIXTURE | admixture | 1.23, 1.3.0 | [13] | biology, genomics, ngs |
AEGeAn | aegean | 0.14.0, 0.16.0 | [14] | biology, genomics |
AFNI | afni | 20.3.00, 2018_04_12, 23.3.09 | [15] | biology, neuroscience, imaging |
AfterQC | afterqc | 0.9.7 | [16] | phylogenetics |
AGAT | agat | 0.4.0 | [17] | phylogenetics |
AGFusion | agfusion | 1.252 | [18] | phylogenetics |
Albacore | albacore | 2.3.1, 2.3.3 | [19] | biology, phylogenetics |
Albumentations | albumentations | 1.0.3 | [20] | ai, image_processing, imaging |
Alder | alder | 1.03 | [21] | biology, genomics |
Alevin-fry | alevin-fry | 0.8.1 | [22] | sequencing, biology |
ALFA | alfa | 1.1.1 | [23] | phylogenetics |
alfred | alfred | 0.2.6 | [24] | web, math |
alienhunter | alienhunter | 1.7 | [25] | biology, sequencing |
AliStat | alistat | 1.12 | [26] | phylogenetics |
alleleCount | allelecount | 20210713 | [27] | biology |
allhic | allhic | 0.9.8 | [28] | genomics, biology |
ALLMAPS | allmaps | 20180117 | [29] | biology, phylogenetics |
ALLPATHS-LG | allpaths | 42316, 44837, 49232 | [30] | biology, ngs |
AlphaFold | alphafold | 2.1.2, 2.3.1, 2.3.2 | [31] | protein, structure, machine_learning |
alphafold2-multimer | alphafold2-multimer-nim | 1.0.0 | [32] | biology |
Alphaimpute | alphaimpute | 0.0.2, 1.9.8.2, 1.9.8.3 | [33] | phylogenetics |
AlphaMate | alphamate | 0.1.1 | [34] | biology |
AlphaPulldown | alphapulldown | 0.30.7, 2.0.0b1, 2.0.0b2 | [35] | protein, structure, machine_learning |
AltAnalyze | altanalyze | 2.1.0 | [36] | biology, genomics |
AMAS | amas | 1.0 | [37] | phylogenetics |
AMBER | amber | 20, 22, 24 | [38] | Chemistry, Molecular Dynamics |
ambertools | ambertools | 23 | [39] | chemistry, molecular_dynamics |
AMICO | amico | 1.0.1, 2.0.1 | [40] | library, imaging, math |
AMOS | amos | 3.1.0 | [41] | biology, genomics, assembly |
AMP | amp | 0.6.1 | [42] | phylogenetics |
amPEPpy | ampeppy | 1.0 | [43] | phylogenetics |
amphora2 | amphora2 | 20140305 | [44] | biology, phylogenetics |
Ampligraph | ampligraph | 2.0.0 | [45] | programming, library, math |
AMPtk | amptk | 1.5.1, 1.5.4, 1.6 | [46] | biology, ngs |
amptorch | amptorch | 20210313 | [47] | phylogenetics |
amrfinderplus | amrfinderplus | 3.10.18, 3.12.8 | [48] | phylogenetics |
AMRPlusPlus | amrplusplus | 20180508 | [49] | phylogenetics |
AMUSE | amuse | 10.0, 13.1.0 | [50] | astronomy |
ancestryhmm | ancestryhmm | 1.0.2 | [51] | genomics, biology |
anchorwave | anchorwave | 1.2.1 | [52] | biology, genomics |
ANDI | andi | 0.15b | [53] | assembly |
ANGSD | angsd | 0.933, 0.940 | [54] | biology, ngs |
annocript | annocript | 2.0 | [55] | phylogenetics |
AnnoTALE | annotale | 1.4.1 | [56] | phylogenetics |
ANNOVAR | annovar | 20150322, 20191024, 20241218 | [57] | biology, genomics |
Ansible | ansible | 2.5.5, 2.8.1 | [58] | workflow_automation |
ANSYS | ansys | 2023R2 | [59] | modeling |
ansysem | ansysem | 17.0, 2022r1, 2023r1 | [60] | physics |
antiSMASH | antismash | 4.1.0, 6.0.1, 7.0.0 | [61] | phylogenetics |
ANTs | ants | 2.2.0, 2.3.4 | [62] | biology, phylogenetics |
anvio | anvio | 6.2, 7.1, 8.0 | [63] | biology |
Appreci8 | appreci8 | 20180530 | [64] | biology, genomics |
apps | clearmap | 2.0 | [65] | biology, neurobiology |
Apptainer | apptainer | 1.2.2, 1.3.1, 1.3.5 | [66] | workflow_automation |
APT | apt | 1.18.0, 1.20.5, 2.11.8 | [67] | biology, genomics |
aquamis | aquamis | 1.4.0 | [68] | biology, genomics |
arb | arb | r19270 | [69] | phylogenetics |
ARC | arc | 1.1.4 | [70] | biology, ngs |
arcashla | arcashla | 0.5.0 | [71] | biology, genetics |
Arcticporechop | arcticporechop | 0.3.2 | [72] | phylogenetics |
Aria2 | aria2 | 1.35.0 | [73] | utility |
ARKS | arks | 1.0.2 | [74] | phylogenetics |
Armadillo | armadillo | 7.900.0, 9.200.6, 9.900.4 | [75] | library, compiler, math |
ARPACK | arpack | 1.0 | [76] | math |
ArrayFire | arrayfire | 3.4.2 | [77] | math |
arriba | arriba | 2.1.0 | [78] | phylogenetics |
ART | art | 20160417, 20160605 | [79] | phylogenetics |
artemis | artemis | 18.1.0 | [80] | biology |
asap | asap | 2.0 | [81] | visualization, biology |
asaq | asaq | 1.0 | [82] | alignment, sequencing, phylogenetics |
ASDEC | asdec | 1.2 | [83] | bioinformatics |
ASE-ANI | ase-ani | 20180712 | [84] | biology, genomics, ngs |
ASHS | ashs | 2.0 | [85] | biology, imaging |
ASPECT | aspect | 2.3.0, 2.5.0 | [86] | geodynamics |
Assembly-stats | assembly-stats | 1.0.1 | [87] | biology, sequencing, genomics |
Assemblytics | assemblytics | 1.2.1 | [88] | phylogenetics |
asset | asset | 20210112 | [89] | sequencing, data_science |
Assexon | assexon | 20190814 | [90] | phylogenetics |
AStalavista | astalavista | 3.2, 4.0 | [91] | biology, genomics |
aster | aster | 1.15, 1.16, 220718 | [92] | biology, data_science, sequencing |
asteroid | asteroid | 1.0 | [93] | genomics |
ASTRAL | astral | 5.6.1, 5.6.2, 5.7.7 | [94] | biology, ngs, phylogenetics |
ASTRID | astrid | 2.2.1 | [95] | phylogenetics |
Astropy | astropy | 2.0.8 | [96] | biology, phylogenetics |
ATAT | atat | 3.23, 3.34 | [97] | material_science |
ATLAS | atlas | 3.10.1, 3.10.2, 3.11.17 | [98] | library, data_science |
Atom | atom | 1.57.0 | [99] | programming |
AtomEye | atomeye | 3 | [100] | material_science |
AtomMan | atomman | 1.3.3 | [101] | phylogenetics |
aTRAM | atram | 2.2.0, 2.4.3 | [102] | math |
Augustus | augustus | 3.3.3, 3.4.0, 3.5.0 | [103] | biology, genomics |
Auto3DEM | auto3dem | 4.05.2 | [104] | image_processing |
AutoDock | autodock | 4.2.6 | [105] | biology |
AutoDock-GPU | autodock-gpu | 1.5.3 | [106] | chemistry |
autodock-vina | autodock-vina | 1.2.3, 1.2.5 | [107] | biology |
Autometa | autometa | 2.2.0, 20190802 | [108] | phylogenetics |
automlsa2 | automlsa2 | 0.8.1 | [109] | phylogenetics, biology, genomics |
AWSCLI | awscli | 2.11.7, 2.2.30 | [110] | utility |
azoo | azoo | 1.3.1 | [111] | phylogenetics |
bactopia | bactopia | 2.2.0 | [112] | genomics |
Badread | badread | 0.1.5 | [113] | phylogenetics |
bakta | bakta | 1.3.3, 1.9.4 | [114] | genomics, biology |
BALi-Phy | bali-phy | 3.4.1, 3.5.0 | [115] | phylogenetics |
BAM-matcher | bam-matcher | 20161021 | [116] | phylogenetics |
Bam-Readcount | bam-readcount | 20150616 | [117] | biology, genomics |
bamaddrg | bamaddrg | 20120326 | [118] | phylogenetics |
BamBam | bambam | 1.0, 1.4 | [119] | biology, genomics |
bamm | bamm | 2.5.0 | [120] | phylogenetics |
bamsnap | bamsnap | 0.2.19 | [121] | phylogenetics |
Bamstats | bamstats | 20140602 | [122] | biology, ngs |
Bamsurgeon | bamsurgeon | 1.2 | [123] | phylogenetics |
bamtofastq | bamtofastq | 1.3.5 | [124] | phylogenetics |
Bamtools | bamtools | 2.5.0, 2.5.1, 2.5.2 | [125] | biology, ngs, sequencing |
bamUtil | bamutil | 1.0.2 | [126] | biology, genomics |
BAPS | baps | 6.0 | [127] | biology, genomics |
Barrnap | barrnap | 0.7, 0.9 | [128] | biology, rna-seq |
Basemount | basemount | 0.15.96, 0.25.2 | [129] | biology, sequencing |
BatMeth2 | batmeth2 | 20210720 | [130] | biology, genomics, mapping |
bax2bam | bax2bam | 0.0.9 | [131] | phylogenetics |
BayArea | bayarea | 1.0.2 | [132] | biology |
BAYENV | bayenv | 2.0 | [133] | biology, phylogenetics |
BayesAss | bayesass | 3.0.4, 3.0.4.2 | [134] | phylogenetics |
bayesass3-snps | bayesass3-snps | 1.1 | [135] | phylogenetics |
BayeScan | bayescan | 2.1 | [136] | biology, variant_calling |
BayesR | bayesr | 20151016 | [137] | biology, phylogenetics |
BayesTraits | bayestraits | 3.0.2 | [138] | phylogenetics |
baypass | baypass | 2.1 | [139] | biology, phylogenetics |
BBMap | bbmap | 38.44, 38.90, 39.06 | [140] | biology, alignment |
bcftools | bcftools | 1.13, 1.15, 1.19 | [141] | biology, ngs |
bcl2fastq | bcl2fastq | 2.16.0.10, 2.20.0.422 | [142] | biology, ngs |
BCLConvert | bclconvert | 4.2.7 | [143] | biology, ngs |
BDG-SeQuila | bdg-sequila | 0.5.5 | [144] | phylogenetics |
BEAGLE | beagle | 4.1, 5.0, 5.2 | [145] | biology, genomics |
BEAR | bear | 20170209 | [146] | biology, genomics |
BEAST | beast | 2.7.0, 2.7.3, 2.7.5 | [147] | biology, phylogenetics |
BEAST2-XML | beast2-xml | 1.0.9 | [148] | phylogenetics |
BEDOPS | bedops | 2.4.30, 2.4.41 | [149] | biology, sequencing, ngs |
BEDTools | bedtools | 2.29.1, 2.29.2, 2.30.0 | [150] | biology, ngs |
Bertini | bertini | 1.6 | [151] | math |
BERTopic | bertopic | 0.14.0, 0.7, 0.8.1 | [152] | machine_learning |
BESST | besst | 2.2.4 | [153] | biology, ngs |
BFAST | bfast | 0.7.0 | [154] | biology, ngs |
BFC | bfc | 1.0 | [155] | genome |
bgenix | bgenix | 1.1.7 | [156] | data_science, genomics |
BIDSCOIN | bidscoin | 3.7.4, 4.3.0 | [157] | neuroscience |
Bifrost | bifrost | 0.2, 1.0.3, 20200225 | [158] | phylogenetics |
BiG-SCAPE | big-scape | 1.1.2, 1.1.9 | [159] | biology, genomics, phylogenetics, pipeline |
bigslice | bigslice | 1.1.1, 2.0.0 | [160] | biology, genomics |
bindash | bindash | 1.0.1, 1.0.2 | [161] | genomics |
BinPacker | binpacker | 1.0 | [162] | biology, rna-seq, assembly |
BinSanity | binsanity | 0.2.6.4 | [163] | biology, genomics |
Bioawk | bioawk | 1.0 | [164] | phylogenetics |
bioBakery | biobakery | 1.8, 3.0.0, 3.1.0 | [165] | phylogenetics |
Biodiverse | biodiverse | 2.1 | [166] | phylogenetics |
Biolite | biolite | 0.3.5.1 | [167] | biology, genomics, variant_calling |
BIOM | biom | 2.1.5, 2.1.6 | [168] | biology, genomics |
BIOMART | biomart | 1.4 | [169] | biology, genomics |
BioNeMo | bionemo | 0.3.1, 1.2, 1.3 | [170] | ai, machine_learning |
Biopieces | biopieces | 2.0 | [171] | phylogenetics |
BirdNET | birdnet | 0.1.2 | [172] | bioinformatics |
BIRDS | fiji-birds | 1.0 | [173] | workflow_automation, utility, imaging |
Bismark | bismark | 0.24.2, 0.7.4, 0.7.7 | [174] | biology, ngs |
Blackfynn | blackfynn | 0.2.7 | [175] | data_mining |
BLASR | blasr | 20130815, 20161215 (5.3), 5.3.2 | [176] | biology, ngs |
Blast2GO | blast2go | 2.5.0-20120705 | [177] | biology, genomics |
Blast2GO CLI | blast2go | 1.3.3 | [178] | biology, genomics |
BLAT | blat | 20121105, 20140318 | [179] | genomics |
blender | blender | 2.77, 3.0.1, 4.0.2 | [180] | graphics |
blink | blink | 0.01 | [181] | genomics |
Blitz | blitz | 0.10, 1.0.2 | [182] | library |
BlobTools | blobtools | 1.0, 2.2, 4.3.5 | [183] | phylogenetics |
bloomfiltertrie | bloomfiltertrie | 0.8.7 | [184] | phylogenetics |
BloomTree | bloomtree | 0.3.5 | [185] | data_mining |
BLUPF90 | blupf90 | 20160604, 20180301, 20190531 | [186] | biology, phylogenetics |
BMGE | bmge | 1.12 | [187] | biology, genomics, phylogenetics |
bmtagger | bmtagger | 3.101 | [188] | genomics, biology |
BOLT-LMM | bolt-lmm | 2.3.4 | [189] | phylogenetics |
BoltzTraP | boltztrap | 1.2.5 | [190] | physics |
Boost | boost | 1.75.0, 1.77.0, 1.82.0 | [191] | programming, library, compiler |
booster | booster | 0.1.2 | [192] | phylogenetics |
botorch | botorch | 0.7.1 | [193] | phylogenetics, biology |
Bowtie | bowtie | 1.2.0, 1.2.3, 1.3.1 | [194] | biology, ngs, sequencing |
Bowtie2 | bowtie2 | 2.3.5.1, 2.4.2, 2.4.5 | [195] | biology, ngs, sequencing |
BoxCLI | boxcli | 2.9.0 | [196] | file_management, web, programming |
BPGA | bpga | 1.2 | [197] | biology, ngs |
BPP | bpp | 4.1.4, 4.3.8, 4.4.1 | [198] | biology, phylogenetics |
BppSuite | bppsuite | 2.3.2 | [199] | genomics |
Bracken | bracken | 1.0.0, 2.5, 2.9 | [200] | biology, phylogenetics |
BrainIAK | brainiak | 0.11 | [201] | imaging |
braker | braker | 3.0.2, 3.0.3, 3.0.8 | [202] | phylogenetics |
BRANCH | branch | 1.8.1 | [203] | biology, ngs, mapping |
BRATNextGen | bratnextgen | 20150505 | [204] | biology, genomics |
BreakDancer | breakdancer | 1.4.5 | [205] | biology, phylogenetics |
breakseq | breakseq | 2.2 | [206] | biology, phylogenetics |
Brewery | brewery | 20191205 | [207] | phylogenetics |
Bridger | bridger | 20141201 | [208] | ngs, genomics, biology |
BRIG | brig | 0.95 | [209] | biology, genomics |
brkraw | brkraw | 0.3.5 | [210] | data_science, imaging |
BRM | brm | 0.3 | [211] | phylogenetics |
Bruker2nifti | bruker2nifti | 1.0.4 | [212] | phylogenetics |
Bsmap | bsmap | 2.87 | [213] | biology, ngs |
Bsoft | bsoft | 1.9.1 | [214] | biology, image_processing |
BSseeker2 | bsseeker2 | 2.1.0, 2.1.8 | [215] | biology, phylogenetics |
bubbleparse | bubbleparse | 20140314 | [216] | biology, phylogenetics |
BUCKy | bucky | 1.4.4 | [217] | biology, phylogenetics |
BUSCO | busco | 4.1.4, 5.2.0 | [218] | biology, genomics |
BWA | bwa | 0.7.7, 0.7.8, 0.7.9a | [219] | biology, ngs |
bwa-mem2 | bwa-mem2 | 2.2.1 | [220] | phylogenetics |
bwa-meth | bwameth | 0.2.7 | [221] | genomics, biology |
BWA-PSSM | bwa-pssm | 0.5.11 | [222] | phylogenetics |
bxh_xcede_tools | bxh_xcede_tools | 1.11.1 | [223] | biology |
BYOBU | byobu | 5.133, 5.92 | [224] | shell |
bzip2 | bzip2 | 1.0.6 | [225] | utility, library |
c-wap | c-wap | 20220624 | [226] | sequencing, genomics, biology |
Cactus | cactus | 2.0.3, 2.0.5, 2.8.0 | [227] | phylogenetics |
CAFE | cafe | 4.1, 5.0.0 | [228] | biology, phylogenetics |
came | came | 0.0.1 | [229] | phylogenetics |
Camino | camino | 20140723 | [230] | biology, neuroscience, imaging |
cammiq | cammiq | 0.1.1 | [231] | genomics, biology |
CAMP | camp | 1.0.0 | [232] | biology, sequencing |
Cantera | cantera | 2.1.1 | [233] | physics |
Canu | canu | 2.0, 2.1, 2.2 | [234] | biology, sequencing |
CANVAS | canvas | 1.40.0.1613 | [235] | phylogenetics |
CAP3 | cap3 | 20120705 | [236] | biology, assembly |
Capnp | capnp | 0.5.3 | [237] | compiler |
captus | captus | 0.9.88, 0.9.91 | [238] | phylogenetics, biology |
CARTA | carta | 2.0 | [239] | image_processing |
CASAVA | casava | 1.8.2 | [240] | biology, ngs |
CASM | casm | 0.2.0 | [241] | physics |
CasOFFinder | casoffinder | 2.4 | [242] | phylogenetics |
CAT | cat | 12 Standalone | [243] | biology |
Catch | catch | 1.4.0 | [244] | biology, genomics, sequencing |
CAVIAR | caviar | 20171218 | [245] | biology, phylogenetics |
CBGpipe | cbgpipe | 20190702 | [246] | phylogenetics |
CCMetagen | ccmetagen | 1.4.0 | [247] | phylogenetics |
CD-HIT | cdhit | 4.6, 4.6.4, 4.6.8 | [248] | biology, genomics |
CDBFasta | cdbfasta | 20181005 | [249] | phylogenetics |
CDNA_Cupcake | cupcake | 20180629, 22.0.0, 9.0.1 | [250] | biology, ngs, sequencing |
CDO | cdo | 1.7.2rc3, 1.9.4 | [251] | climate |
CDRT | cdrt | 23.10 | [] | machine_learning |
celescope | celescope | 2.1.0 | [252] | biology, sequencing, genomics |
celescope_atac | celescope_atac | 1.2.0 | [253] | biology, sequencing, genomics |
CellProfiler | cellprofiler | 3.1.9, 4.1.3, 4.2.6 | [254] | phylogenetics |
CellRanger | cellranger | 7.0.1, 7.2.0, 8.0.0 | [255] | biology, ngs, rna-seq |
CellRanger-ARC | cellranger-arc | 2.0.1, 2.0.2 | [256] | biology, ngs, rna-seq |
CellRanger-ATAC | cellranger-atac | 1.2.0 | [257] | biology, ngs, rna-seq |
CellRanger-DNA | cellranger-dna | 1.0.0, 1.1.0 | [258] | biology, ngs, rna-seq, genomics |
Centrifuge | centrifuge | 1.0.3, 1.0.4b | [259] | biology, phylogenetics |
CFITSIO | cfitsio | 3.370 | [260] | library, compiler |
CGAL | cgal | 5.02, 5.5.2, 5.6 | [261] | library, math |
CGATools | cgatools | 1.6.0.43 | [262] | biology, ngs |
cgmaptools | cgmaptools | 0.1.1, 0.1.2 | [263] | phylogenetics |
cgmlst | cgmlst | 0.2 | [264] | phylogenetics |
cgmlstfinder | cgmlstfinder | 1.0 | [265] | genetics |
CGView | cgview | 1.0.2 | [266] | phylogenetics |
CHARMM | charmm | 4b2, c48b2, c49b1 | [267] | chemistry, simulation |
ChartDirector | libchartdir | 5.1.0 | [268] | library, data_science |
CheckM | checkm | 1.0.4, 1.0.7, 1.1.2 | [269] | biology, genomics |
checkv | checkv | 1.0.1 | [270] | biology, genomics |
chewbbaca | chewbbaca | 3.3.0 | [271] | biology, genomics |
chewiesnake | chewiesnake | 3.0.0 | [272] | biology, genomics |
Chimera | chimera | 1.12 | [273] | biology, modeling |
Chipyard | chipyard | 1.0 | [274] | simulation |
Chopper | chopper | 0.8.0 | [275] | bioinformatics |
Chromeister | chromeister | 1.5a | [276] | biology, genomics |
ChromEvol | chromevol | 2.0, 3.0 | [277] | biology, ngs |
CIALIGN | cialign | 1.1.4 | [278] | bioinformatics |
CIMS | cims | 4.1.2 | [279] | biology, genomics |
CIRCexplorer | circexplorer | 1.1.10 | [280] | biology, rna-seq |
CIRCexplorer2 | circexplorer2 | 2.3.5, 2.3.8 | [281] | phylogenetics |
circexplorer3 | circexplorer3 | 01172021 | [282] | RNA-Seq |
Circlator | circlator | 1.5.5 | [283] | phylogenetics |
Circleator | circleator | 1.0.2 | [284] | phylogenetics |
circompara2 | circompara2 | 0.1.2.1 | [285] | phylogenetics |
Circos | circos | 0.63-pre11, 0.69-2, 0.69-9 | [286] | biology, genomics, ngs |
circtools | circtools | 1.2.1 | [287] | biology |
CIRI | ciri | 2.0.6 | [288] | phylogenetics |
ciriquant | ciriquant | 1.1.2 | [289] | phylogenetics |
CisGenome | cisgenome | 2.0 | [290] | biology, genomics |
cisTEM | cistem | 1.0.0 | [291] | phylogenetics |
Clairvoyante | clairvoyante | 1.02 | [292] | phylogenetics |
Clann | clann | 3.2.3 | [293] | biology, phylogenetics |
clara | clara | v4.0 | [294] | ai, machine_learning |
CLARK | clark | 1.2.2-b, 1.2.3 | [295] | biology, genomics |
clean | clean | 1.0.1 | [296] | protein, machine_learning |
CLHEP | clhep | 2.2.0.1 | [297] | physics |
CLIFinder | clifinder | 4.1 | [298] | biology, phylogenetics |
ClinicaDL | clinicadl | 1.0.4, 1.2.0 | [299] | biology, imaging, machine_learning |
clipkit | clipkit | 1.3.0 | [300] | genomics, biology |
CLIPper | clipper | 2.1.0 | [301] | phylogenetics |
CLIPSeqTools | clipseqtools | 0.1.7 | [302] | biology, sequencing |
CliqueSNV | cliquesnv | 2.0.3 | [303] | biology, phylogenetics |
ClonalFrame | clonalframe | 1.1, 1.2 | [304] | biology, ngs, phylogenetics |
ClonalFrameML | clonalframeml | 1.0, 1.11 | [305] | biology, ngs, phylogenetics |
CloudCompare | cloudcompare | 2.10.3 | [306] | visualization |
Clover | clover | 2.0 | [307] | biology, genomics, assembly |
CLUMPP | clumpp | 1.1.2 | [308] | biology |
ClustalO | clustalo | 1.2.0 | [309] | biology, alignment |
ClustalW | clustalw | 2.1 | [310] | biology, alignment |
cluster3 | cluster3 | 1.52a | [311] | biology, genomics |
Clview | clview | 20130402 | [312] | biology |
CMake | cmake | 3.21.3, 3.26.4, 3.30.5 | [313] | programming |
CMS | cms | 20170518, 20240429 | [314] | biology |
CMWP | cmwp | 140518 | [315] | biology, genomics |
CNCI | cnci | 20180305 | [316] | phylogenetics |
CNSpipeline | cnspipeline | 20170827 | [317] | phylogenetics |
CNV-Seq | cnvseq | 20110715, 20140812 | [318] | biology, genomics |
CNV-Sim | cnv-sim | 0.9.2 | [319] | biology, phylogenetics |
CNVkit | cnvkit | 0.9.6 | [320] | phylogenetics |
CNVnator | cnvnator | 0.3.2 | [321] | biology, genomics |
cobra-tf | cobra-tf | 0.1 | [322] | fluid_dynamics |
Cobretti | cobretti | 1.0 | [323] | GeneExpression |
CodonPhyML | codonphyml | 20150303 | [324] | phylogenetics |
Coevol | coevol | 1.3c, 1.4b, 1.6 | [325] | biology, phylogenetics |
Cogent | cogent | 2.1 | [326] | biology, phylogenetics |
COLMAP | colmap | 3.6 | [327] | modeling |
CoMap | comap | 1.4.1 | [328] | biology, genomics |
combined-pvalues | combined-pvalues | 0.50.6 | [329] | statistics, bioinformatics |
COMEBIN | comebin | 1.0.4 | [330] | biology, genomics |
Comp-D_MPI | comp-d_mpi | 1.0 | [331] | statistics |
Compacta | compacta | 1.02 | [332] | biology, genomics |
COMSOL | comsol | 6.2, 6.2.04, 6.3 | [333] | simulation |
Concaterpillar | concaterpillar | 1.8a | [334] | phylogenetics |
CONCOCT | concoct | 1.1.0 | [335] | biology, genomics |
Conda | conda | 24.3.0, 24.7.1 | [336] | programming |
Conefor | conefor | 2.7.3 | [337] | software |
CONN | conn | 22a | [338] | imaging |
CONNECT | connect | 20200614 | [339] | phylogenetics |
connectomemapper3 | connectomemapper3 | 3.0.0-rc1 | [340] | phylogenetics |
ConPADE | conpade | 1.0 | [341] | phylogenetics |
Conpair | conpair | 20161010, 20180624 | [342] | biology, phylogenetics |
Consed | consed | 23.0, 25.0, 29.0 | [343] | biology, genomics |
CONSEL | consel | 0.20 | [344] | biology, phylogenetics |
ContaVect | contavect | 0.2 | [345] | biology, phylogenetics |
Convert3D | convert3d | 1.1.0 | [346] | imaging, utility |
Coot | coot | 0.9.5 | [347] | modeling |
CoPTR | coptr | 1.1.6 | [348] | biology |
Coreutils | coreutils | 8.23, 8.28 | [349] | utility |
Corset | corset | 1.06 | [350] | biology, ngs |
Counterr | counterr | 0.1, 20230501 | [351] | phylogenetics |
Coverm | coverm | 0.6.1 | [352] | biology, genomics, ngs |
covNMR | covnmr | 2014 | [353] | chemistry, biology |
cp2k | cp2k | 2024.1, 7.0.0 | [354] | imaging |
CPAT | cpat | 3.0.2 | [355] | phylogenetics |
cpc | cpc | 2.0 | [356] | phylogenetics |
CPLEX | cplex | 12.6.2, 12.7, 12.9 | [357] | climate |
Crass | crass | 1.0.1 | [358] | biology, assembly |
crest | crest | 12.2, 2.12, 3.0 | [359] | chemistry |
crisflash | crisflash | 1.2.0 | [360] | phylogenetics |
CRISP | crisp | 20181122, 20240419 | [361] | phylogenetics |
CRISPRanalyzer | crispranalyzer | 1.50 | [362] | biology, genomics, ngs |
CRISPRCasFinder | crisprcasfinder | 4.2.17 | [363] | phylogenetics |
CRISPResso2 | crispresso2 | 20220811 | [364] | genomics, sequencing, biology |
CrossMap | crossmap | 0.3.9, 0.6.3 | [365] | biology, genomics |
crossmapper | crossmapper | 1.1.1 | [366] | phylogenetics |
Crux | crux | 1.40 | [367] | biology, spectroscopy |
cryodrgn | cryodrgn | 2.3.0, 3.4.2 | [368] | biology |
CryptoMiniSat | cryptominisat | 5.0.1 | [369] | math |
csubst | csubst | 1.3.0 | [370] | Biology, Phylogenetics |
csvpad | csvpad | 1.2 | [371] | data science |
csvtk | csvtk | 0.23.0, 0.30.0 | [372] | biology |
ctk | ctk | 1.1.4 | [373] | biology, genomics |
CUBE | cube | 4.4 | [374] | library, compiler, math |
CUDA | cuda | 12.2.2, 12.3.2, 12.4.1 | [375] | programming, library, graphics |
Cufflinks | cufflinks | 2.1.1, 2.2.1, 2.2.1.1 | [376] | biology, ngs, sequencing |
cuOpt | cuopt | 22.12 | [377] | Accelerated AI Logistics and Route Optimization |
cupy | cupy | 8.3.0 | [378] | phylogenetics |
cutadapt | cutadapt | 1.18, 2.8, 3.4 | [379] | biology, ngs |
CutRunTools | cutruntools | 20200104 | [380] | phylogenetics |
cvbio | cvbio | 3.0.0 | [381] | phylogenetics |
CViT | cvit | 1.3 | [382] | programming, library |
CWLtool | cwltool | 1.0.20190906, 2.0.20200126, 3.0.20210124104916 | [383] | workflow_automation, scheduler |
cx_oracle | cxoracle | 8.3.0 | [384] | database, utility |
CycleGan | cyclegan | 20201015 | [385] | phylogenetics |
Cytoscape | cytoscape | 3.10.2, 3.4.0 | [386] | biology, ngs, phylogenetics |
cyvcf2 | cyvcf2 | 20230728 | [387] | library |
d2go | d2go | 20210702 | [388] | machine_learning, ai |
dadi | dadi | 2.1.1 | [389] | phylogenetics |
DAKOTA | dakota | 6.15, 6.8, 6.8-gui | [390] | math |
DALIGNER | daligner | 1.0 | [391] | biology, phylogenetics |
dammit | dammit | 1.0rc2 | [392] | biology, phylogenetics |
dancemapper | dancemapper | 1.0.0 | [393] | machine learning |
dapars | dapars | 1.0.0 | [394] | genomics, biology |
darwin-gpu | darwin-gpu | 20190115 | [395] | genomics, alignment |
DASTool | dastool | 1.1.0, 1.1.2 | [396] | biology, phylogenetics |
datamash | datamash | 1.1.0 | [397] | math |
DAWGPAWS | dawgpaws | 1.0 | [398] | biology, phylogenetics |
dbcanlight | dbcanlight | 1.1.0 | [399] | biology, annotation |
DCC | dcc | 0.4.4 | [400] | biology, ngs |
Dcmstack | dcmstack | 0.6.2 | [401] | biology, imaging |
DCMTK | dcmtk | 3.6.0 | [402] | biology, neuroscience, imaging |
dDocent | ddocent | 2.7.8 | [403] | phylogenetics |
ddprotocol | ddprotocol | 20230405 | [404] | biology, machine learning |
DDSCAT | ddscat | 7.3.0 | [405] | astronomy |
DDT | ddt | 20.0, 20.2, 23.0 | [406] | programming |
DealII | dealii | 8.3.0, 9.3.1, 9.5.1 | [407] | library |
DeconSeq | deconseq | 0.4.3 | [408] | biology, phylogenetics |
decontaMiner | decontaminer | 1.4 | [409] | genomics, biology |
DECX | decx | 20180205 | [410] | phylogenetics |
DeepARG | deeparg | 1.0.1 | [411] | phylogenetics |
deepbgc | deepbgc | 0.1.18 | [412] | phylogenetics |
Deepcoil | deepcoil | 2.0.1 | [413] | sequencing, biology |
deepfri | deepfri | 03312021 | [414] | machine learning, biology |
DeepGS | deepgs | 1.2 | [415] | phylogenetics |
DeepLabCut | deeplabcut | 2.0.7-gpu, 2.1.1, 2.2.1 | [416] | phylogenetics |
deeplexicon | deeplexicon | 1.2.0 | [417] | RNAseq |
DeePMD-kit | deepmd-kit | 2.1.11 | [418] | molecular dynamics, deep learning |
deepmd-kit | ngc-deepmd-kit | 2.1.1 | [419] | Molecular Dynamics and Machine learning |
DeepMD-LAMMPS | deepmd-lammps | 2.2.0-02Aug23 | [420] | molecular Dynamics |
deepmicrobes | deepmicrobes | 20200219 | [421] | biology, genomics, machine_learning |
DeepMReye | deepmreye | 01192022 | [422] | library, biology |
DeepPicker | deeppicker | 20161102 | [423] | imaging |
deepsig | deepsig | 1.2.5 | [424] | biology |
deepTools | deeptools | 2.4.3, 3.1.1, 3.5.2 | [425] | biology, ngs |
deepvariant | deepvariant | 1.4.0, 1.5.0, 1.6.1 | [426] | biology, genomics, sequencing, machine_learning |
deFusion | defusion | 20200305 | [427] | phylogenetics |
Delft3D | delft3d | 4.06.01, 7545 | [428] | physics |
Delineate | delineate | 1.2.2 | [429] | biology, genomics |
Delly | delly | 0.7.7, 0.7.8, 1.1.5 | [430] | biology, phylogenetics |
delucs | delucs | 20220512 | [431] | sequencing, genomics, machine_learning |
DeNoGAP | denogap | 1.0 | [432] | biology, phylogenetics, ngs |
DERIVA | deriva | 1.5.0 | [433] | phylogenetics |
deSALT | desalt | 1.5.6 | [434] | biology, genomics, sequencing |
Desmond | desmond | 6.9 | [435] | biology |
Detectron2 | detectron2 | 0.4, 0.5, 0.6 | [436] | library |
DeTiN | detin | 1.7.5.9 | [437] | imaging, ngs, genomics |
DEVIDER | devider | 0.0.1 | [438] | biology, genomics, ngs, nanopore |
DEXTRACTOR | dextractor | 1.0 | [439] | biology, sequencing |
Diamond | diamond | 2.1.1, 2.1.3, 2.1.8 | [440] | biology, genomics |
DIANN | diann | 1.8.1 | [441] | protein, structure |
diCal2 | dical2 | 2.2.0.1 | [442] | biology, phylogenetics |
diffdock | diffdock-nim | 2.0 | [443] | docking, drug discovery |
diffDomain | diffdomain | 1.0.0 | [444] | bioinformatics |
diffReps | diffreps | 1.55.4 | [445] | biology |
disbatch | disbatch | 2.5 | [446] | software |
DISCOVAR de novo | discovardenovo | 52488 | [447] | biology, ngs, assembly |
DiscoVista | discovista | 20180906 | [448] | phylogenetics |
discvrseq | discvrseq | 1.3.10 | [449] | biology, phylogenetics |
Distruct | distruct | 2.3 | [450] | phylogenetics |
DIYABC | diyabc | 1.0.4.43b, 2.0.3, 2.1.0 | [451] | biology, phylogenetics |
DL_POLY | dlpoly | 1.9 | [452] | molecular_dynamics |
Dlib | dlib | 19.19 | [453] | phylogenetics |
DNA Clust | dnaclust | 3.0 | [454] | biology, genomics |
DOCK | dock | 6.7, 6.8, 6.9 | [455] | chemistry |
DoGFinder | dogfinder | 20201103 | [456] | phylogenetics |
dorado | dorado | 0.7.0, 0.7.2, 0.8.2 | [457] | genomics |
DosageConvertor | dosageconvertor | 1.0.3 | [458] | biology |
DOT | dot | 2.0 | [459] | biology, chemistry |
Doxygen | doxygen | 1.12.0, 1.8.3.1, 1.9.7 | [460] | programming, documentation |
DP_GP_cluster | dp_gp_cluster | 0.1 | [461] | bioinformatics |
dragmap | dragmap | 1.2.1 | [462] | phylogenetics, sequencing, biology |
dragonflye | dragonflye | 1.0.12 | [463] | sequencing, genomics |
dram | dram | 1.3 | [464] | biology, genomics, annotation |
DRAP | drap | 1.91 | [465] | biology, phylogenetics |
dRep | drep | 2.3.2, 3.4.2 | [466] | phylogenetics |
dretools | dretools | 0.0.1.20 | [467] | rna-seq |
drishti | drishti | 3.2 | [468] | visualization |
Dropseq | dropseq | 2.4.0 | [469] | phylogenetics |
DS9 | saoimageds9 | 7.5, 8.0.1 | [470] | imaging |
DScribe | dscribe | 1.2.0 | [471] | machine_learning |
dsistudio | dsistudio | 20210123, 20220803, 20240311 | [472] | imaging |
DSK | dsk | 2.1.0, 2.3.0 | [473] | biology, ngs |
DSRC | dsrc | 2.0 | [474] | phylogenetics |
DSSAT | dssat | 4.6 | [475] | simulation |
DSSP | dssp | 2.2.1, 3.0.0 | [476] | molecular_dynamics |
DSuite | dsuite | 0.4, 0.4-r41, 0.4-r49 | [477] | biology, genomics |
DTI-TK | dtitk | 2.3.1 | [478] | imaging |
dtiprep | dtiprep | 0.1.1 | [479] | phylogenetics |
duchamp | duchamp | 1.6.2 | [480] | phylogenetics |
DVGfinder | dvgfinder | 3.1 | [481] | genomics, search, sequencing |
dx-toolkit | dx-toolkit | 0.347.0 | [482] | biology |
dynamicDBG | dynamicdbg | 20181003 | [483] | phylogenetics |
Dynare | dynare | 4.4.3 | [484] | math |
dynasor | dynasor | 2.0 | [] | Molecular_Dynamics |
ea-utils | eautils | 1.04.807.18, 1.1.2.537 | [485] | biology, genomics, ngs |
EAGLE | eagle | 2.0 | [486] | phylogenetics |
eagle-rc | eagle-rc | 1.1.1 | [487] | phylogenetics |
Earlgrey | earlgrey | 4.2.4 | [488] | biology |
ECE | ece | 1.2 | [489] | physics |
ecopcr | ecopcr | 0.5.0 | [490] | Biology |
eddy-squeeze | eddy-squeeze | 1.0.8 | [491] | data_science, visualization |
EDirect | edirect | 10.7, 12.2 | [492] | biology, phylogenetics |
EDTA | edta | 1.9.6, 2.1.0 | [493] | genomics |
Edyeet | edyeet | 0.1, 0.3 | [494] | phylogenetics |
EEGLAB | eeglab | 12.0.2.1b, 13.2.2b, 13.4.4b | [495] | biology |
effectorp | effectorp | 2.0.1, 3.0 | [496] | biology, annotation |
eGene-MVN | egene-mvn | 0.1 | [497] | biology, genomics |
eggNOG-mapper | eggnog-mapper | 2.0.1, 2.1.12, 2.1.6 | [498] | phylogenetics |
Ego4D | ego4d | 1.3.2 | [499] | image processing |
EGSnrc | egsnrc | 2019 | [500] | phylogenetics |
EIGEN3 | eigen3 | 3.4.0 | [501] | libraries, mathematics |
EIGENSOFT | eigensoft | 5.0.1, 6.0.1, 6.1.4 | [502] | biology |
Elastix | elastix | 4.9.0, 5.1.0 | [503] | phylogenetics |
ELPA | elpa | 2019.11.001 | [504] | library, compiler, math |
elPrep | elprep | 4.1.4 | [505] | phylogenetics |
Emacs | emacs | 27.2, 28.2 | [506] | programming, language |
Email Alert Service | email_storage_alert | 1.0.0 | [507] | file_management |
EMAN2 | eman2 | 2.22, 2.31 | [508] | image_processing |
EMBOSS | emboss | 6.6.0 | [509] | biology |
Embree | embree | 3.6.1 | [510] | graphics |
EMC | emc | 9.4.3 | [511] | simulation |
emerald | emerald | 0.1 | [512] | biology |
EMMAX | emmax | 20100307, 20120210 | [513] | biology, ngs, mapping |
emu | emu | 3.4.5 | [514] | phylogenetics |
EnergyPlus | energyplus | 9.3.0 | [515] | simulation |
enrichm | enrichm | 0.6.5 | [516] | biology |
Ensembl Tools | ensembl_tools | 100, 80 | [517] | biology |
enTAP | entap | 0.6.1.2, 20160416 | [518] | biology, phylogenetics |
EPACTS | epacts | 3.2.6, 3.4.2, 3.4.2.hg38 | [519] | biology, genomics |
EpiNano | epinano | 1.2.0 | [520] | biology, ngs |
epiteome | epiteome | 1.0 | [521] | phylogenetics |
epoch | epoch | 4.7.3 | [522] | astronomy |
eQTLA | eqtla | 1.1 | [523] | biology, genomics |
eQtlBma | eqtlbma | 1.2.2, 1.3.0r20140820 | [524] | biology, genomics |
Erpin | erpin | 5.5.4 | [525] | biology, phylogenetics |
esmf | esmf | 8.3.0), 8.7.0) | [526] | geospatial |
ESOM | esom | 1.1 | [527] | biology, phylogenetics |
ESPRESSO | espresso | 7.0, 7.1, 7.2 | [528] | chemistry, modeling |
ESPRIT | esprit | 2009-nogap, 201102 | [529] | biology |
ETE3 | ete3 | 3.0.0, 3.1.1 | [530] | biology, phylogenetics |
ETE4 | ete | 4.0.0 | [531] | biology, phylogenetics |
EUKulele | eukulele | 2.0.7 | [532] | alignment, biology, genomics |
EVidenceModeler | evidencemodeler | 1.1.1 | [533] | phylogenetics |
Evigene | evigene | 20180730, 20200520 | [534] | phylogenetics |
EvoLSTM | evolstm | 20220103 | [535] | biology |
ExaBayes | exabayes | 1.5 | [536] | phylogenetics |
Exonerate | exonerate | 2.2.0, 2.4.0 | [537] | biology, genomics |
ExpansionHunter | expansionhunter | 4.0.2 | [538] | biology, genomics |
ExpansionHunterDenovo | expansionhunterdenovo | 0.9.0 | [539] | biology, genomics |
export2graphlan | export2graphlan | 0.22 | [540] | statistics, mapping, visualization |
eXpress | express | 1.3.1, 1.5.1 | [541] | biology, ngs |
ezaai | ezaai | 1.0 | [542] | biology, phylogenetics |
face_morpher | face_morpher | 20190630 | [543] | phylogenetics |
face_recognition | face_recognition | 1.2.2 | [544] | phylogenetics |
fairseq | fairseq | 0.12.2 | [545] | modeling, ai |
falco | falco | 1.2.1 | [546] | biology, sequencing |
FALCON | falcon | 20161027, 20161222, 20190601 | [547] | biology, ngs, sequencing |
FALCON_unzip | falcon_unzip | 20161222 | [548] | biology |
fanc | fanc | 0.9.28 | [549] | biology, genomics, ngs |
faqcs | faqcs | 2.10 | [550] | Genomics, biology |
FAR | far | 2.15 | [551] | biology, genomics |
FAST | fast | 1.06 | [552] | biology, phylogenetics |
fast-gep | fast-gep | 1.0 | [553] | phylogenetics |
Fast-Plast | fast-plast | 1.2.6 | [554] | biology, phylogenetics |
fast5tools | fast5tools | 0.3.1 | [555] | phylogenetics, biology |
FASTA | fasta | 34.26.5, 36.3.6d | [556] | biology, genomics |
fastai | fastai | 2.1.5, 2.6.3, 2.7.10 | [557] | Machine_Learning |
FastANI | fastani | 1.1, 1.34 | [558] | phylogenetics |
fastchaos | fastchaos | 0.1.0 | [559] | sequencing |
FastGEAR | fastgear | 20161216 | [560] | biology, genomics |
Fastix | fastix | 0.1.0 | [561] | biology, ngs |
FastML | fastml | 3.0 | [562] | biology, phylogenetics |
Fastp | fastp | 0.20.0, 0.22.0, 0.23.4 | [563] | biology, ngs |
FASTphase | fastphase | 1.4.8 | [564] | phylogenetics |
FastPlast | fastplast | 1.2.8 | [565] | phylogenetics |
fastq-pair | fastq-pair | 1.0 | [566] | phylogenetics |
FastQ-Screen | fastq-screen | 0.14.0 | [567] | phylogenetics |
Fastq-tools | fastq-tools | 0.8 | [568] | biology, ngs |
FastQC | fastqc | 0.11.7, 0.12.1, 0.9.6 | [569] | biology, ngs |
FastqPuri | fastqpuri | 1.0.7 | [570] | phylogenetics |
FastQTL | fastqtl | 2.184 | [571] | phylogenetics |
FASTRAL-constrained | fastral-constrained | 20211108 | [572] | phylogenetics |
fastsimcoal | fastsimcoal2 | 2.6.0.3, 2.7.0.2 | [573] | biology, phylogenetics |
FastSpar | fastspar | 0.0.4 | [574] | biology, genomics |
fastStructure | faststructure | 20150112, 20240221 | [575] | biology, genomics |
FastTree | fasttree | 2.1.11 | [576] | biology, phylogenetics |
FastUniq | fastuniq | 1.1 | [577] | biology, phylogenetics |
fastv | fastv | 0.10.0 | [578] | bioinformatics, sequencing |
Fastx Toolkit | fastx_toolkit | 0.0.13.2, 0.0.14 | [579] | biology, ngs |
fcGENE | fcgene | 1.0.7, 1.0.7.1 | [580] | biology, genomics, variant_calling |
FDSTools | fdstools | 1.2.0 | [581] | phylogenetics |
fdupes | fdupes | 1.51 | [582] | file_management |
febio | febio | 2.9.1 | [583] | biomechanics |
FEELnc | feelnc | 0.1.1 | [584] | phylogenetics |
feh | feh | 3.9.1 | [585] | utility, image_processing |
FEniCS | fenics | 2018.1.0 | [586] | biology, phylogenetics |
Ferret | ferret | 6.82 | [587] | visualization, geospatial, climate |
FFmpeg | ffmpeg | 4.3.1, n6.1, n7.2 | [588] | audio, visualization |
FFTW | fftw | 3.3.6, 3.3.7, 3.3.8 | [589] | library, compiler, math |
fgbio | fgbio | 0.5.0, 0.7.0 | [590] | phylogenetics |
FGMP | fgmp | 1.0.1 | [591] | phylogenetics |
FGTPartitioner | fgtpartitioner | 1.0.1 | [592] | genomics |
FIGARO | figaro | 1.1.2 | [593] | phylogenetics |
Fiji | fiji | 2.0.0rc59 | [594] | image_processing |
Filtlong | filtlong | 0.2.0 | [595] | biology, phylogenetics |
Finder | finder | 20210503, 20210609 | [596] | biology, search |
finemap | finemap | 1.4 | [597] | phylogenetics |
fineRADstructure | fineradstructure | 0.3.2 | [598] | phylogenetics |
finesse | finesse | 2.3.1 | [599] | simulation |
Firefox | firefox | 1.0 | [600] | linux, web |
fit-sne | fit-sne | 1.2.1 | [601] | phylogenetics |
FLAIR | flair | 1.5, 2.0 | [602] | phylogenetics |
flairNLP | flairnlp | 0.10 | [603] | visualization, language |
flappie | flappie | 1.1.0, 2.1.3 | [604] | phylogenetics |
FLASh | flash | 1.2.10, 1.2.11 | [605] | biology, genomics |
FLEA | flea | 2.0.0 | [606] | phylogenetics |
flex | flex | 2.6.4 | [607] | programming |
Flexbar | flexbar | 2.3, 2.34, 3.5.0 | [608] | biology, genomics, ngs |
FLEXLm | flexlm | 1.0 | [609] | utility |
flopp | flopp | 0.2.0 | [610] | genomics |
FlowCraft | flowcraft | 1.4.1 | [611] | phylogenetics |
Fluent | fluent | 17.2, 19.1, 2020R1 | [612] | fluid_dynamics |
Flye | flye | 2.9.1, 2.9.2, 2.9.3 | [613] | biology, ngs |
fMRIPrep | fmriprep | 20.2.3, 23.1.3, 23.1.4 | [614] | data_mining |
foldseek | foldseek | 9.427df8a | [615] | bioinformatics |
forecasting | forecasting | 0.10.3 | [616] | Machine_Learning, Data_Science |
ForeSeqs | foreseqs | 1.0.4 | [617] | phylogenetics |
forwardgenomics | forwardgenomics | 1.0 | [618] | phylogenetics |
fpocket | fpocket | 4.0.2 | [619] | sequencing, biology |
fqtools | fqtools | 20160224 | [620] | biology, ngs, sequencing |
FragGeneScan | fraggenescan | 1.16 | [621] | biology, genomics |
FRAMA | frama | 20151019 | [622] | biology |
FrameDP | framedp | 1.2.2 | [623] | biology, sequencing |
FRAPOSA | fraposa | 20200421 | [624] | phylogenetics |
FreeBayes | freebayes | 1.3.1, 1.3.2, 1.3.7 | [625] | biology, genomics |
freecad | freecad | 0.20.2 | [626] | modeling |
freesasa | freesasa | 2.1.2 | [627] | molecular_dynamics, biology |
Freesurfer | freesurfer | 7.2.0, 7.3.2, 7.4.1 | [628] | biology, neuroscience, imaging |
Freyja | freyja | 1.3.1, 1.3.4, 1.3.8 | [629] | biology, phylogenetics, sequencing |
FSA | fsa | 1.15.9 | [630] | phylogenetics |
FSL | fsl | 6.0.4, 6.0.5, 6.0.6 | [631] | biology, neuroscience, imaging |
fslmrs | fslmrs | 1.1.10 | [632] | spectroscopy, metabolomics |
funannotate | funannotate | 1.8.5, 1.8.7, 1.8.9 | [633] | phylogenetics |
fusion_twas | fusion_twas | 20210218 | [634] | phylogenetics |
GAL | gal | 20180906 | [635] | biology, genomics, annotation |
Galaxy | galaxytools | 1.0 | [636] | biology |
galaxyml | galaxyml | 0.10.0 | [637] | library, machine_learning |
GAML | gaml | 20150610 | [638] | biology, genomics, assembly |
GapCloser | gapcloser | 1.12r6 | [639] | biology, genomics, ngs |
GapFiller | gapfiller | 1.10, 1.11 | [640] | biology, genomics |
gapseq | gapseq | 1.2 | [641] | chemistry, biology |
garfield | garfield | 2 | [642] | genomics |
GARLI | garli | 2.0, 2.01 | [643] | biology, phylogenetics |
GASVPro | gasvpro | 201310 | [644] | biology, ngs |
GATE | gate | 7.0 | [645] | library |
GATK | gatk | 4.1.9.0, 4.3.0.0, 4.4.0.0 | [646] | biology, ngs |
Gaussian | gaussian | 09 D.01, 16, 16-c02 | [647] | chemistry |
Gawk | gawk | 4.2.0 | [648] | utility |
Gblocks | gblocks | 0.91b | [649] | biology, alignment |
GCC | gcc | 7.3.0, 8.2.0, 9.3.0 | [650] | compiler |
GCE | gce | 1.0.2 | [651] | biology, genomics |
gcloud | gcloud | 471.0.0 | [652] | cloud, google, cli |
gcnenv | gcnenv | 1.13 | [653] | library, math |
GCT | gct | 6.2.1 | [654] | file_management, utility |
GCTA | gcta | 1.26.0, 1.92.4beta, 1.93.2beta | [655] | biology, genomics, variant_calling |
GDAL | gdal | 2.3.1, 3.7.0, 3.9.0 | [656] | geospatial, library |
GDB | gdb | 8.3, 9.2 | [657] | programming |
GDC-Client | gdc-client | 1.0.1, 1.5.0 | [658] | biology, sequencing, ngs |
GDrive | gdrive | 2.1.0 | [659] | utility, file_management |
GDSL | gdsl | 1.18 | [660] | library |
Geant4 | geant4 | 4.10, 4.10.03, 4.10.5 | [661] | physics |
geant4 | geant4 | 11.0.2, 4-11.0.3 | [662] | physics, simulation |
GEM | gem | 20130406 | [663] | biology, ngs, sequencing |
gem5 | gem5 | 2.0 | [664] | simulation |
GEMMA | gemma | 0.98.1, 0.98.5 | [665] | biology, genomics |
gemma_llm | gemma_llm | 1 | [666] | library, math |
genblastg | genblastg | 1.39 | [667] | biology, genomics |
GeneMark-ES | genemark_es | 4.68, 4.69, 4.71 | [668] | biology, genomics |
GeneMarkS | genemark_s | 2012.04 | [669] | biology, genomics |
GeneMarkS-T | genemark_s | 3.10.001 | [670] | biology, genomics |
GenePainter | genepainter | 2.0.4 | [671] | biology, phylogenetics |
GeneRax | generax | 1.2.2 | [672] | phylogenetics |
Generic Mapping Tools | gmt | 6.4.0 | [673] | physics, biology |
GeneSeqer | geneseqer | 2014-02-26 | [674] | biology, genomics |
genesis | genesis | 2.1.2, 2.1.2-cpu, 2.1.4 | [675] | Physics |
genesum | genesum | 0.1.0 | [676] | biology, genomics |
GeneTorrent | genetorrent | 3.8.7 | [677] | biology, file_management |
genewalk | genewalk | 1.5.3 | [678] | phylogenetics |
GenGen | gengen | 1.0.1 | [679] | biology, phylogenetics |
genmap | genmap | v1.3.0 | [680] | Gene mapping, biology |
geNomad | genomad | 1.5.1 | [681] | biology, genomics |
Genome STRiP | genomestrip | 2.00.1602 | [682] | biology, genomics, ngs |
Genome_Graph_Annotation | genome_graph_annotation | 20190131 | [683] | phylogenetics |
GenomeScope2 | genomescope2 | 2.0 | [684] | phylogenetics |
GenomeThreader | genomethreader | 1.7.3 | [685] | phylogenetics |
GenomeTools | genometools | 1.5.7, 1.5.9 | [686] | biology |
genomic-fluidity | genomic-fluidity | 20151109 | [687] | phylogenetics |
GenomicConsensus | genomicconsensus | 2.3.3 | [688] | biology, phylogenetics |
GenomicNeuralnet | genomic-neuralnet | 20161030 | [689] | phylogenetics |
GenomicTools | genomictools | 2.7.0 | [690] | biology, ngs, chip-seq, rna-seq |
GenotypeHarmonizer | genotypeharmonizer | 1.4.18 | [691] | biology |
Genrich | genrich | 0.5 | [692] | phylogenetics |
GenSel | gensel | 4.90 | [693] | genomics |
geomxngspipeline | geomxngspipeline | 3.1.1.5 | [694] | NGS |
geopython | geopython | 1.0.0, 1.0.1, 1.0.2 | [695] | programming, geospatial |
GEOS | geos | 3.3.8, 3.6.2 | [696] | library, data_science |
GeP | gep | 2.1 | [697] | biology, phylogenetics |
gepard | gepard | 1.40.0, 2.1.0 | [698] | phylogenetics |
Gephi | gephi | 0.10.0 | [699] | visualization, image_processing |
Gerbil | gerbil | 1.11 | [700] | phylogenetics |
get_homologues | get_homologues | 3.3.3 | [701] | biology, genomics |
GetOrganelle | getorganelle | 1.7.3.5, 1.7.5.0 | [702] | phylogenetics |
GFam | gfam | 1.1 | [703] | biology, genomics, annotation |
GFATools | gfatools | 0.5 | [704] | bioinformatics |
GFF-Ex | gff-ex | 2.3 | [705] | phylogenetics |
GFF3toolkit | gff3toolkit | 2.0.3 | [706] | phylogenetics |
gffcompare | gffcompare | 0.12.2 | [707] | phylogenetics |
gffread | gffread | 0.11.8, 0.12.7, 0.9.8c | [708] | biology |
Gflags | gflags | 2.2.1, 20150520 | [709] | web, library |
GFOLD | gfold | 1.1.4 | [710] | biology, rna-seq |
ggsashimi | ggsashimi | 0.5.0 | [711] | phylogenetics |
GHOST-MP | ghost-mp | 1.3.4 | [712] | phylogenetics |
Ghostscript | ghostscript | 9.22 | [713] | documentation |
giggle | giggle | 20221212 | [714] | Genomics |
Gimmemotifs | gimmemotifs | 0.18.0 | [715] | biology, genetics |
Giotto | giotto | 0.1.0 | [716] | phylogenetics |
giraf | giraf | 1.02 | [717] | sequencing, biology |
Git | git | 2.14.1, 2.30.1 | [718] | revision_control |
git-filter-repo | git-filter-repo | 2.33.0 | [719] | phylogenetics |
Github Cli | github-cli | 2.40.1 | [720] | revision_control |
Gkeyll | gkeyll | 2.0 | [721] | Plasma Physics |
glactools | glactools | 1.0.8 | [722] | phylogenetics |
Glimmer | glimmer | 3.02 | [723] | biology, annotation |
GlimmerHMM | glimmerhmm | 3.0.4 | [724] | biology, annotation |
GLMsingle | glmsingle | 1.0 | [725] | imaging |
glnexus | glnexus | 1.4.1 | [726] | programming |
Globus | globus | 2.1.3, 3.13.0, 3.18.0 | [727] | file_management |
glog | glog | 0.3.5 | [728] | web, library |
GLPK | glpk | 4.55, 4.65 | [729] | programming |
Glueviz | glueviz | 0.15.2 | [730] | phylogenetics |
GMAP | gmap | 20180212, 20180212_sse2, 20190610 | [731] | biology, genomics, ngs |
GMcloser | gmcloser | 1.6 | [732] | biology, ngs |
GMP | gmp | 6.1.2, 6.3.0 | [733] | library |
gnuastro | gnuastro | 0.21 | [734] | astronomy |
GnuPlot | gnuplot | 5.2.2, 5.2.3, 5.4.1 | [735] | graphics, math |
Go | go | 1.15.4, 1.18.3, 1.21.0 | [736] | language |
goatools | goatools | 1.2.3 | [737] | biology, ontology |
GOMAP | gomap | 1.3, 1.4 | [738] | biology, ngs |
GoPHY | gophy | 201030 | [739] | phylogenetics |
Gosling | gosling | 0.2.2 | [740] | genomics, visualization |
gotcloud | gotcloud | 1.17.5 | [741] | phylogenetics |
GPA | gpa | 1.1 | [742] | phylogenetics |
GPhoCS | gphocs | 1.2.3 | [743] | phylogenetics |
gptl | gptl | 20140212 | [744] | utility |
GPTL | gptl | 20140212 | [745] | utility |
Gpufit | gpufit | 20201127 | [746] | phylogenetics |
Grace | grace | 5.1.22 | [747] | graphics, statistics |
GRACKLE | grackle | 3.1 | [748] | library, compiler, astronomy |
Grackle | grackle | 3.2.1 | [749] | library, compiler, astronomy |
GrADS | grads | 2.0.1 | [750] | geospatial, math |
Graftm | graftm | 0.12.2 | [751] | phylogenetics |
GramCluster | gramcluster | 1.3 | [752] | biology, sequencing |
graph-tool | graph-tool | 2.32 | [753] | phylogenetics |
Graph_annotation | graph_annotation | 0.1 | [754] | phylogenetics |
graphaligner | graphaligner | 1.0.11, 1.0.16 | [755] | genomics |
GraPhlAn | graphlan | 1.1.3 | [756] | phylogenetics |
GraphMap2 | graphmap2 | 0.6.5 | [757] | phylogenetics |
GRAPHMB | graphmb | 0.2.5 | [758] | biology, genomics |
GraphSplitting | graphsplitting | 2.4 | [759] | phylogenetics |
graphtyper | graphtyper | 2.7.2 | [760] | phylogenetics |
GraphViz | graphviz | 2.38.0, 2.46.1 | [761] | biology, neuroscience, imaging |
GRASS | grass | 7.0, 7.4 | [762] | geospatial |
grf | grf | 1.0.0 | [763] | genomics |
Grib_api | grib_api | 1.10.1, 1.15.1, 1.26.1 | [764] | compiler, library |
GRIDSS | gridss | 2.6.2 | [765] | phylogenetics |
GROCSVs | grocsvs | 0.2.5 | [766] | phylogenetics |
GROMACS | gromacs | 2022.3, 2023.2, 2024.4 | [767] | chemistry, molecular_dynamics |
GroopM | groopm | 0.3.5 | [768] | biology, phylogenetics |
Groovy | groovy | 2.4.15 | [769] | programming |
Gscripts | gscripts | 1.1 | [770] | biology |
GSEA | gsea | 4.2.2 | [771] | biology, genomics |
GSL | gsl | 2.6, 2.7, 2.7.1 | [772] | library, data_science |
GSNP | gsnp | 1.0 | [773] | biology, ngs |
gsp | gsp | 05192017 | [774] | biology |
GTAHunter | gtahunter | 20200106 | [775] | phylogenetics |
GTDBTk | gtdbtk | 2.0.0, 2.1.0, 2.3.2 | [776] | phylogenetics |
GTOOL | gtool | 0.7.5 | [777] | phylogenetics |
GUAVA | guava | 1.0 | [778] | phylogenetics |
Gubbins | gubbins | 2.4.1, 3.2.1, 3.3.0 | [779] | phylogenetics |
guideseq | guideseq | 1.0.2 | [780] | sequencing, genomics, biology, data_science |
guile | guile | 2.2.2 | [781] | programming |
GULP | gulp | 4.4, 5.0 | [782] | material_science |
guppy | guppy | 6.1.7, 6.4.2, 6.4.3 | [783] | phylogenetics |
Gurobi | gurobi | 10.0.0, 11.0.1, 9.5.1 | [784] | math, programming |
GWAMA | gwama | 2.2.2 | [785] | phylogenetics |
Gzip | gzip | 1.10 | [786] | compression |
hacdivsel | hacdivsel | 1.4.1 | [787] | genomics, biology |
Hail | hail | 0.2.130, 0.2.77 | [788] | biology, genomics |
hal | hal | 2.1 | [789] | phylogenetics |
HALC | halc | 1.1 | [790] | biology, phylogenetics |
halla | halla | 0.8.17 | [791] | phylogenetics |
HaMStR | hamstr | 13.2.3, 13.2.4, v8b | [792] | biology, genomics |
hapbin | hapbin | 1.3.0 | [793] | biology, genomics |
HapCompass | hapcompass | 0.7.7 | [794] | imaging, ngs, genomics |
HAPCUT | hapcut | 0.7 | [795] | biology, assembly |
HapCUT2 | hapcut2 | 1.3.3 | [796] | biology, genomics, sequencing |
hapdup | hapdup | 0.6 | [797] | phylogenetics, biology |
haphpipe | haphpipe | 1.0.3 | [798] | phylogenetics, biology |
Haploflow | haploflow | 0.1 | [799] | biology, phylogenetics |
Haplomerger2 | haplomerger2 | 20180603 | [800] | biology, genomics |
HAPLOSWEEP | haplosweep | 1.0 | [801] | biology, phylogenetics |
happy | happy | 0.3.14 | [802] | phylogenetics, biology |
hapQTL | hapqtl | 1.00 | [803] | biology |
hapsembler | hapsembler | 2.21 | [804] | biology, assembly |
harvesttools | harvesttools | 1.2 | [805] | phylogenetics, biology |
HASLR | haslr | 0.8a1 | [806] | phylogenetics |
hclust2 | hclust2 | 1.0.0 | [807] | statistics, mapping |
HDF4 | hdf4 | 4.2.11 | [808] | library, data_science |
HDF5 | hdf5 | 1.8.19, 1.8.20, 1.8.9 | [809] | library, data_science |
hecaton | hecaton | 0.5.1 | [810] | genomics, biology |
HELEN | helen | 20200516 | [811] | phylogenetics |
HelitronScanner | helitronscanner | 1.1 | [812] | phylogenetics |
helixer | helixer | 0.3.3 | [813] | Genomics |
herro | herro | 0.1.0 | [814] | Genomics |
hgraph2graph | hgraph2graph | 20210428 | [815] | chemistry |
hgtector | hgtector | 2.0 | [816] | biology, sequencing |
hhsuite | hhsuite | 3.3.0 | [817] | |
Hi-Corrector | hi-corrector | 1.2 | [818] | biology, ngs, sequencing |
hic-lift | hic-lift | 06112023 | [819] | genomics |
HiC-Pro | hic-pro | 3.0.0, 3.1.0 | [820] | biology, pipeline, genomics |
Hifiasm | hifiasm | 0.19.9, 0.4, 0.8 | [821] | phylogenetics |
Hificnv | hificnv | 0.1.7 | [822] | biology, genomics, ngs |
hillerlab | hillerlab | 20240819 | [823] | phylogenetics |
hiphase | hiphase | 1.4.0 | [824] | biology, ngs |
HipSTR | hipstr | 0.7 | [825] | phylogenetics |
HISAT2 | hisat2 | 2.2.1, 2.2.1-3n, 20230203 | [826] | biology, alignment, ngs |
hivtrace | hivtrace | 1.5.0 | [827] | biology,alignment |
HLAminer | hlaminer | 1.3.1, 1.4 | [828] | biology, phylogenetics |
HMM-FRAME | hmm-frame | 20140724 | [829] | phylogenetics |
HmmCleaner | hmmcleaner | 0.180750 | [830] | phylogenetics |
HMMER | hmmer | 3.2.1, 3.3.2, 3.4 | [831] | biology, genomics |
hmmer2go | hmmer2go | 0.18.1 | [832] | phylogenetics, biology |
HMMRATAC | hmmratac | 1.2.10 | [833] | phylogenetics |
HoCoRT | hocort | 1.2.2 | [834] | RNA-Seq, QC |
HOMER | homer | 4.10, 4.11, 4.8 | [835] | biology, sequencing, ngs |
homopolish | homopolish | 0.3.3, 0.4.1 | [836] | genomics, biology |
HOOMD | hoomd | 2.1.7 | [837] | library, math |
HPL | hpl | 2.1 | [838] | programming, performance_analysis |
hpsandbox | hpsandbox | 1.0.0 | [839] | Programming |
HTMLDoc | htmldoc | 1.8.28, 1.9.3 | [840] | documentation, web |
HTSeq | htseq | 0.11.2, 2.0.3 | [841] | biology, ngs |
HUMAnN | humann | 2.8.1, 3.8 | [842] | sequencing, biology |
humann2 | humann2 | 0.11.2, 2.8.1 | [843] | phylogenetics |
hxtorch | hxtorch | 0.8 | [844] | imaging |
hyb | hyb | 20141126, 20200815 | [845] | biology, ngs, rna-seq |
hybkit | hybkit | 0.3.4, 0.3.5, 0.3.6 | [846] | biology |
HybPiper | hybpiper | 2.1.5, 2.1.6, 2.3.0 | [847] | biology, phylogenetics |
HyDe | hyde | 0.4.3 | [848] | phylogenetics |
hylite | hylite | 2.0.2 | [849] | genomics, biology |
Hyper-Gen | hypergen | 0.1.0 | [850] | Programming |
HyPhy | hyphy | 2.5.4, 2.5.7, 2.5.8 | [851] | biology, genomics |
HYPRE | hypre | 2.15.1, 2.18.2, 2.19.0 | [852] | math |
iAnnotateSV | iannotatesv | 1.0.6, 1.0.9 | [853] | biology, phylogenetics |
iaps | iaps | 02012023 | [854] | programming |
iAssembler | iassembler | 1.3.2 | [855] | biology, assembly |
IBDmix | ibdmix | 1.0.1 | [856] | biology |
ibdne | ibdne | 20150815 | [857] | biology, ngs |
icommands | icommands | 3.3.1 | [858] | utility |
IDBA-MT | idba-mt | 1.0 | [859] | biology, ngs |
IDBA-UD | idba-ud | 1.1.1, 1.1.1-512, 1.1.1-512-mem | [860] | genomics, phylogenetics |
IDL | idl | 8.3 | [861] | language, programming, data_science |
IDR | idr | 2.0.3 | [862] | phylogenetics |
IGB | igb | 8.4.1 | [863] | biology, genomics |
igBLAST | igblast | 1.5.0, 1.7.0 | [864] | biology |
IGoR | igor | 1.4.0 | [865] | phylogenetics |
iGTP | igtp | 1.1 | [866] | biology, phylogenetics |
IGV | igv | 2.3.91, 2.4.16, 2.8.6 | [867] | biology, ngs, phylogenetics |
illumina-utils | illumina-utils | 2.11 | [868] | phylogenetics |
Illumiprocessor | illumiprocessor | 2.0.9 | [869] | phylogenetics |
IM and IMa | ima | 20091217 | [870] | biology, genomics |
Ima2 | ima2 | 20120827 | [871] | biology, genomics |
IMa2p | ima2p | 20170712 | [872] | biology, phylogenetics |
IMA3 | ima3 | 22Aug18 | [873] | molecular_dynamics |
ImageJ | imagej | 1.48 | [874] | imaging |
imagej2 | imagej2 | 09302022 | [875] | image processing, imaging |
ImageMagick | imagemagick | 7.0.8-20 | [876] | imaging |
Imaginaire | imaginaire | 20201229 | [877] | imaging, visualization, ai, machine_learning |
IMOD | imod | 4.7.15, 4.9.10 | [878] | image_processing |
imoka | imoka | 1.0 | [879] | biology, genomics |
impg | impg | 0.1.0 | [880] | biology, alignment |
IMPUTE2 | impute2 | 2.3.2 | [881] | phylogenetics |
IMPUTE5 | impute5 | 1.1.5, 1.2.0 | [882] | biology, math |
INDELible | indelible | 1.03 | [883] | phylogenetics |
Infernal | infernal | 1.1.1, 1.1.4 | [884] | biology, alignment |
INLA | inla | 20160718, 20170620 | [885] | statistics, modeling, programming |
InParanoid | inparanoid | 4.1 | [886] | biology |
Inspector | inspector | 1.0.2 | [887] | biology, genomics |
InStruct | instruct | 20160723 | [888] | phylogenetics |
Intel Compilers and Libraries | intel | 2023.0.0, 2023.2.0, 2024.1.0 | [889] | language, programming, library, math, compiler |
Intel MPI | impi | 5.1.1 | [890] | programming, library |
InterProScan | iprscan | 5.68, 5.69, 5.72 | [891] | biology |
intervene | intervene | 0.6.2 | [892] | biology, phylogenetics |
Intrasom | intrasom | 1.0 | [893] | python |
IOAPI | ioapi | 3.1, 3.2 | [894] | climate |
IPOPT | ipopt | 3.12.10, 3.12.6 | [895] | library, compiler, math |
ipyrad | ipyrad | 0.9.102, 0.9.53, 0.9.94 | [896] | phylogenetics |
IQ-TREE | iq-tree | 2.2.2.7, 2.3.2, 2.3.6 | [897] | biology, phylogenetics |
IRAP | irap | 0.8.1p7 | [898] | biology, ngs |
irep | irep | 1.10 | [899] | biology, genomics |
IRFinder | irfinder | 1.2.0, 1.3.0, 1.3.1 | [900] | biology, rna-seq |
isce2 | isce2 | 2.6.3 | [901] | library |
ISCE3 | isce3 | 0.23.0 | [902] | library |
isONclust | isonclust | 0.0.6 | [903] | phylogenetics |
isonclust2 | isonclust2 | 2.3 | [904] | rna-seq |
IsoSel | isosel | 1.0 | [905] | phylogenetics |
IsoSeq3 | isoseq3 | 3.7.0, 3.8.2, 4.0.0 | [906] | biology, ngs |
ISOWN | isown | 20180820 | [907] | phylogenetics |
isPcr | ispcr | 3.3 | [908] | biology, phylogenetics |
ITK | itk | 3.20.1, 4.10.1 | [909] | biology |
ITK-SNAP | itksnap | 3.0.0, 3.8.0 | [910] | biology, neuroscience, imaging |
ITSx | itsx | 1.1b | [911] | phylogenetics |
iupred2a | iupred2a | 1.0 | [912] | biology |
IVA | iva | 1.0.11 | [913] | phylogenetics |
iVar | ivar | 1.3.1, 1.4.2 | [914] | biology |
Jabba | jabba | 1.0 | [915] | biology, phylogenetics |
JACUSA | jacusa | 1.2.0 | [916] | biology, ngs, phylogenetics |
JAGS | jags | 3.3.0, 3.4.0, 4.2.0 | [917] | statistics |
janus | janus | 20240412 | [918] | biology |
Jasmine | jasmine | 1.1.4 | [919] | phylogenetics |
jasp | jasp | 0.14.3 | [920] | statistics |
jasper | jasper | 1.0.4 | [921] | biology |
jbrowse2 | jbrowse2 | 1.7.4 | [922] | web |
JCVI | jcvi | 0.8.12, 1.0.13, 1.2.10 | [923] | phylogenetics |
JDK | java | 20, 23, 9.0.1 | [924] | programming |
Je | je | 1.0 | [925] | biology, ngs |
Jellyfish | jellyfish | 2.2.4, 2.2.6, 2.3.0 | [926] | biology, ngs |
jModelTest | jmodeltest | 2.1.1 | [927] | biology, genomics, phylogenetics |
jo | jo | 1.3 | [928] | utility |
jq | jq | 1.6 | [929] | utility |
juicer | juicer | 1.22.01, 2.0 | [930] | genomics |
Julia | julia | 1.7.3, 1.8.2, 1.9.2 | [931] | programming, language, statistics |
Jupyter | jupyter | 6.2.0, 6.5.2, 6.5.4 | [932] | programming |
jutils | jutils | 1.0 | [933] | genomics, biology |
JVARKIT | jvarkit | 20180405 | [934] | biology, phylogenetics |
Kaiju | kaiju | 1.6.2, 1.7.2 | [935] | biology, phylogenetics |
KaKs | kaks | 1.2, 2.0 | [936] | biology, genomics, phylogenetics |
Kalign | kalign | 3.3.1 | [937] | biology, sequencing, alignment |
kallisto | kallisto | 0.46.2, 0.48.0, 0.50.1 | [938] | biology, ngs, rna-seq |
khmer | khmer | 2.0, 2.1 | [939] | biology, ngs |
KIM | kim | 1.7.2, 1.8.2, 1.9.3 | [940] | simulation |
kimmingloci | skimmingloc | 1.0.0 | [941] | pipeline mapping, biology |
KING | king | 2.1.2, 2.3.0 | [942] | biology, genomics |
KisSplice | kissplice | 2.4.0-p1 | [943] | biology, RNA |
KLayout | klayout | 0.26.7 | [944] | phylogenetics |
kma | kma | 20230106 | [945] | alignment |
KMC | kmc | 3.1.0, 3.1.1, 3.2.1 | [946] | phylogenetics |
kmerdb | kmerdb | 1.9.2 | [947] | genomics, biology |
kmerfreq | kmerfreq | 4.0 | [948] | biology, genomics |
KMOS | kmos | 0.3.21 | [949] | phylogenetics |
kneaddata | kneaddata | 0.12.0, 0.7.4, 0.9.0 | [https:https://github.com/biobakery/kneaddata] | biology, genomics |
knime | knime | 4.7.3 | [950] | data science |
Knitro | knitro | 12.2.0 | [951] | math |
KofamScan | kofamscan | 1.3.0 | [952] | phylogenetics |
kover | kover | 2.0.3 | [953] | phylogenetics |
Kraken | kraken | 2.0.8b, 2.1.2, 2.1.3 | [954] | biology, ngs |
KrakenTools | krakentools | 1.2 | [955] | biology, ngs |
KrakenUniq | krakenuniq | 0.5.8, 0.7.3, 1.0.4 | [956] | phylogenetics |
Krona | krona | 2.8.1, 20161019 | [957] | biology |
ksnp | ksnp | 3.021, 4.0 | [958] | biology, phylogenetics, variant_calling |
Ksrates | ksrates | 1.1.1 | [959] | genomics, biology |
kvarq | kvarq | 0.12.2 | [960] | biology |
LACHESIS | lachesis | 2.1 | [961] | phylogenetics |
Lambda | lambda | 0.9.4, 1.0.3, 2.0.0 | [962] | biology, sequencing, phylogenetics |
LAMMPS | lammps | 3Nov2022, 7Aug19, 7Dec15 | [963] | molecular_dynamics |
LAMMPS-PPA | lammps-ppa | 23Jun2022 | [964] | molecular Dynamics |
LAMP | lamp | 2.5 | [965] | biology, genomics |
laneta | laneta | 20220517, 20220808, 20220812 | [966] | biology |
langdetect | langdetect | 1.0.9 | [967] | language, utility |
LAPACK | lapack | 3.11.0, 3.8.0 | [968] | programming, library, compiler |
Last | last | 916, 979 | [969] | biology, sequencing, alignment |
LAStools | lastools | 20200114 | [970] | image_processing |
LASTZ | lastz | 1.02.00, 1.03.02, 1.04.00 | [971] | biology, ngs |
Lazypipe | lazypipe | 1.2 | [972] | genomics |
LazyPredict | lazypredict | 0.2.8 | [973] | phylogenetics |
lbzip | lbzip | 2.5 | [974] | compression |
LCModel | lcmodel | 6.3 | [975] | biology, spectroscopy |
ldak | ldak | 5.2 | [976] | phylogenetics, biology |
ldblockshow | ldblockshow | 1.40 | [977] | biology |
LDhat | ldhat | 2.2a | [978] | biology, genomics |
ldsc | ldsc | 1.0.1 | [979] | genomics, biology |
leafaudio | leafaudio | 0.1.0 | [980] | machine_learning, audio |
LEfSe | lefse | 20180219 | [981] | phylogenetics |
LEMON | liblemon | 1.2.3 | [982] | library |
LFMM | lfmm | 1.4, 1.5 | [983] | biology, phylogenetics |
libgfortran | libgfortran | 3.0.0 | [984] | programming |
Libint | libint | 2.5.0, 2.5.0b | [985] | library |
libMesh | libmesh | 1.5.0 | [986] | math |
libunistring | libunistring | 0.9.7 | [987] | library |
libvips | libvips | 8.5.4 | [988] | image_processing |
LIBXC | libxc | 4.3.4, 6.2.2, 7.0.0 | [989] | library, math |
LIBXSMM | libxsmm | 1.13 | [990] | library, compiler, math |
LIBZMQ | libzmq | 4.3.1 | [991] | library |
Liftoff | liftoff | 1.4.2, 1.6.2 | [992] | phylogenetics |
Lighter | lighter | 1.1.3 | [993] | genome |
LIGR | ligr | 2.05 | [994] | biology, assembly |
LillyMol | lillymol | 6.1 | [995] | |
lima | lima | 2.0.0, 2.2.0, 2.7.1 | [996] | phylogenetics |
lingua | lingua | 1.0.1 | [997] | language, utility |
LINKS | links | 1.8.5, 1.8.6 | [998] | biology, genomics |
Linksbrowser | linksbrowser | 2.14 | [999] | web |
LIQA | liqa | 1.0.0, 1.1.16 | [1,000] | phylogenetics |
llama | llama | 2, 3 | [1,001] | library, math |
llama-alex | llama | alex | [1,002] | library, math |
llava | llava | 1.6 | [1,003] | Machine Learning |
LMAP | lmap | 1.0.2 | [1,004] | biology, phylogenetics |
lncScore | lncscore | 1.0.2 | [1,005] | biology, phylogenetics |
lobSTR | lobstr | 4.0.6 | [1,006] | biology, phylogenetics |
localbrainage | localbrainage | 20210415 | [1,007] | biology, machine_learning |
localizer | localizer | 1.0.4, 1.0.5 | [1,008] | phylogenetics |
LocusZoom | locuszoom | 1.4 | [1,009] | phylogenetics |
LoFreq | lofreq | 2.1.3.1 | [1,010] | phylogenetics |
LongQC | longqc | 1.2.0c | [1,011] | phylogenetics |
LongRanger | longranger | 2.1.5, 2.2.2 | [1,012] | biology, phylogenetics |
longshot | longshot | 0.4.5 | [1,013] | genomics |
LongStitch | longstitch | 1.0.3 | [1,014] | genomics, biology |
LoRDEC | lordec | 0.9 | [1,015] | phylogenetics |
LoRMA | lorma | 0.3, 0.5 | [1,016] | biology, ngs |
loter | loter | 1.0 | [1,017] | genomics, |
LRBinner | lrbinner | 0.1 | [1,018] | biology, genomics |
lrgapcloser | lrgapcloser | 09042018 | [1,019] | biology |
LS-DYNA | ls-dyna | 700, 711, 901 | [1,020] | physics |
LSD2 | lsd2 | 1.6.5 | [1,021] | phylogenetics |
ltr_finder | ltr_finder | 1.07 | [1,022] | biology, phylogenetics |
LTRRetriever | ltrretriever | 2.1, 2.5, 2.9.0 | [1,023] | biology, phylogenetics |
Lua | lua | 5.3.2, 5.3.4, 5.4.6 | [1,024] | programming, language |
Lucene | pylucene | 7.7.1, 9.1.0 | [1,025] | programming, search |
lumpy-sv | lumpy | 0.2.1, 0.2.13, 0.3.1 | [1,026] | biology, genomics |
LZO | lzo | 2.09 | [1,027] | library, compression |
M5nr | m5tools | 20121126 | [1,028] | biology, genomics |
Macaulay2 | macaulay2 | 1.15 | [1,029] | phylogenetics |
MACH | mach | 1.0.18 | [1,030] | biology, genomics, ngs |
Mach2VCF | mach2vcf | 20150515 | [1,031] | biology |
Macrel | macrel | 1.3.0 | [1,032] | biology, genomics |
MACS | macs | 2.0.10, 2.1.2, 2.2.7.1 | [1,033] | biology, chip-seq |
MafFilter | maffilter | 1.3.0 | [1,034] | phylogenetics |
MAFFT | mafft | 7.490, 7.505, 7.520 | [1,035] | biology, sequencing |
MAGeCK | mageck | 0.5.9.4 | [1,036] | phylogenetics |
MAGeCK-VISPR | mageck-vispr | 0.5.6 | [1,037] | phylogenetics |
MAGeCKFlute | mageckflute | 1.14.0 | [1,038] | phylogenetics |
Magenta | magenta | 2.1.2 | [1,039] | phylogenetics |
magicblast | magicblast | 1.6.0 | [1,040] | genomics, biology |
MAGMA-GWAS | magma-gwas | 1.09 | [1,041] | phylogenetics |
magpurify | magpurify | 2.1.2 | [1,042] | genomics |
magus | magus | 20220121 | [1,043] | sequencing, alignment |
MAJIQ | majiq | 2.2, 2.3, 2.5.7 | [1,044] | phylogenetics |
Maker | maker | 2.31.10, 2.31.6, 3.01.03 | [1,045] | biology |
MAnorm | manorm | 20120316 | [1,046] | biology, phylogenetics |
MANTA | manta | 1.6.0 | [1,047] | phylogenetics |
mantis | mantis | 1.0.4 | [1,048] | phylogenetics |
mapclassify | mapclassify | 2.4.2 | [1,049] | statistics, mapping, geospatial |
mapdamage | mapdamage | 2.2.1 | [1,050] | ngs, sequencing, biology |
MapThin | mapthin | 1.11 | [1,051] | phylogenetics |
Maq | maq | 0.7.1 | [1,052] | biology, ngs |
MarginPolish | marginpolish | 1.0.0 | [1,053] | phylogenetics |
MARK | mark | 2.0.1 | [1,054] | data_science, math |
MarkerMiner | markerminer | 20150710 | [1,055] | biology, genomics |
Mash | mash | 1.1, 2.3 | [1,056] | biology, genomics |
MasHmap | mashmap | 2.0 | [1,057] | phylogenetics |
mashtree | mashtree | 1.2.0 | [1,058] | genomics, biology |
maskrc-svg | maskrc-svg | 0.5 | [1,059] | genomics |
MASS | mass | 1.1.1 | [1,060] | genomics, biology |
MASSMINE | massmine | 0.10.0, 0.11.0, 0.9.5 | [1,061] | data_mining |
MaSuRCA | masurca | 4.0.8, 4.0.9, 4.1.0 | [1,062] | biology, alignment |
Mathematica | mathematica | 13.1, 14.0 | [1,063] | math |
MATLAB | matlab | 2023b, 2024a, 2024b | [1,064] | math, language |
MATS | mats | 4.0.2, 4.1.0, 4.2.0 | [1,065] | biology, ngs, rna-seq |
matt | matt | 1.3.1 | [1,066] | |
Mauve | mauve | 2.3.1 | [1,067] | biology, ngs, genomics |
mawk | mawk | 1.3.4-20150503 | [1,068] | language |
maxbin | maxbin | 2.1.1 | [1,069] | biology, ngs |
Maxima | maxima | 5.41.0 | [1,070] | math |
MC | mc | 4.6.1 | [1,071] | shell |
mCarts | mcarts | 1.0.2 | [1,072] | biology, genomics, math |
mccortex | mccortex | 1.0 | [1,073] | phylogenetics |
mcfost | mcfost | 4.1.07 | [1,074] | astronomy |
MCL | mcl | 12-135, 14-137 | [1,075] | biology, genomics |
MCNP | mcnp | 6, 6.1, 6.3.0 | [1,076] | physics |
MCNPX | mcnpx | 2.7.0 | [1,077] | physics |
MCR | mcr | 2020a, 2020b, 2023b | [1,078] | math, language |
MCScanX | mcscanx | 20130328 | [1,079] | biology, phylogenetics |
mdanalysis | mdanalysis | 1.1.1 | [1,080] | physics, biology |
MECAT | mecat | 20180308 | [1,081] | phylogenetics |
Medaka | medaka | 1.7.2, 1.8.0, 2.0 | [1,082] | biology, phylogenetics |
Medusa | medusa | 1.6 | [1,083] | phylogenetics |
MEGA | mega | 11.0.13, 7.0.26 | [1,084] | biology, phylogenetics |
Mega2 | mega2 | 4.9.2, 6.0.0 | [1,085] | biology, phylogenetics |
MEGAHIT | megahit | 1.1.1, 1.1.4, 1.2.9 | [1,086] | biology, phylogenetics |
Megalodon | megalodon | 2.0.0, 2.4.1 | [1,087] | ngs, genomics |
MEGAN | megan | 6.23.4, 6.25.9, 6.4.15 | [1,088] | biology, ngs |
MEGASAT | megasat | 1.0 | [1,089] | phylogenetics |
Megraft | megraft | 1.0.2 | [1,090] | biology, sequencing |
MELD | meld | 0.4.19, 0.5.0, 0.5.9 | [1,091] | chemistry, molecular_dynamics |
MELTING | melting | 4.3.1 | [1,092] | biology, genomics, rna |
MEME | meme | 5.0.2, 5.0.5, 5.4.1 | [1,093] | biology, sequencing |
MentaLiST | mentalist | 0.1.3 | [1,094] | biology, phylogenetics |
Meraculous | meraculous | 2.0.5 | [1,095] | biology, ngs |
Mercurial | mercurial | 4.8.2 | [1,096] | revision_control |
merge_peaks | merge_peaks | 0.1.0 | [1,097] | workflow_automation |
Merlin | merlin | 1.1.2 | [1,098] | biology, variant_calling |
Merqury | merqury | 1.1, 1.3 | [1,099] | phylogenetics |
Meryl | meryl | 1.0 | [1,100] | phylogenetics |
MeShClust | meshclust | 1.2.0 | [1,101] | biology |
Meshroom | meshroom | 2019.2.0 | [1,102] | phylogenetics |
Meson | meson | 1.2.3 | [1,103] | biology, ngs, sequencing |
MET | met | 10.0 | [1,104] | climate, modeling |
Meta-Marc | meta-marc | 1.0.0 | [1,105] | phylogenetics |
Meta-Tissue | meta-tissue | 0.4 | [1,106] | biology, genomics |
MetaBAT | metabat | 0.32.4, 2.13 | [1,107] | biology, genomics |
MetaBCC-LR | metabcc_lr | 2.0.0 | [1,108] | biology, genomics |
Metabin | metabin | 1.0 | [1,109] | genomics |
metabolic | metabolic | 4.0 | [1,110] | phylogenetics |
MetaCherchant | metacherchant | 0.1.0 | [1,111] | biology, phylogenetics |
MetaCluster | metacluster | 5.0b | [1,112] | biology, genomics |
MetaCompare | metacompare | 20181016 | [1,113] | phylogenetics |
metacrast | metacrast | 20200309 | [1,114] | phylogenetics |
Metaeuk | metaeuk | 6.0 | [1,115] | phylogenetics |
MetaGeneMark | metagenemark | 2.10, 3.26 | [1,116] | biology, genomics |
METAL | metal | 20110325 | [1,117] | biology, ngs, genomics |
MetaLAFFA | metalaffa | 1.0.0 | [1,118] | phylogenetics |
MetaMaps | metamaps | 20201207 | [1,119] | phylogenetics |
METANNOT | metannot | 20171129 | [1,120] | phylogenetics |
Metaphlan | metaphlan | 4.0.6, 4.1.0, 4.1.1 | [1,121] | phylogenetics |
MetaPhlAn2 | metaphlan2 | 2.7.7 | [1,122] | biology, phylogenetics |
MetaPhysicl | metaphysicl | 1.0.0 | [1,123] | math, astronomy, simulation |
Metashape | metashape | 1.8.4, 2.1.1 | [1,124] | |
MetaSV | metasv | 0.5.4 | [1,125] | biology, phylogenetics, ngs |
MetaVelvet | metavelvet | 1.2.06 | [1,126] | biology, genomics |
metaWRAP | metawrap | 1.2 | [1,127] | phylogenetics |
Metaxa2 | metaxa2 | 2.1.1, 2.1.3, 2.2.3 | [1,128] | biology, ngs, sequencing |
methylartist | methylartist | 1.3.0 | [1,129] | biology |
MethylDackel | methyldackel | 0.5.0, 0.6.1 | [1,130] | phylogenetics |
methylpy | methylpy | 1.2.9 | [1,131] | biology, phylogenetics |
Metilene | metilene | 0.2.8 | [1,132] | biology, genomics, methylation |
METIS | metis | 5.1.0, 5.2.1 | [1,133] | utility |
Mfannot | mfannot | 20180405 | [1,134] | biology, phylogenetics |
mfold | mfold | 3.6 | [1,135] | biology, structure, rna |
mg-rast | mg-rast | 20150919 | [1,136] | biology, genomics |
MGEfinder | mgefinder | 1.0.5 | [1,137] | phylogenetics |
MGERT | mgert | 1.0.1 | [1,138] | phylogenetics |
MGEScan | mgescan | 20160416 | [1,139] | biology, genomics |
MGLTools | mgltools | 1.5.7 | [1,140] | biology, visualization |
Mgs2amr | mgs2amr | 2.0.1 | [1,141] | genomics |
MHAP | mhap | 1.6 | [1,142] | biology, sequencing |
MHCflurry | mhcflurry | 1.4.3 | [1,143] | phylogenetics |
MIA | mia | 20130201 | [1,144] | biology, ngs |
micop | micop | 03312022 | [1,145] | genomics |
MicrobeAnnotator | microbeannotator | 2.0.5 | [1,146] | annotation, biology |
MIDAS | midas | 1.3.2, 20160830 | [1,147] | biology, phylogenetics |
MIGRATE-N | migraten | 4.2.14, 4.4.4, 5.0.4 | [1,148] | biology, genomics |
Mikado | mikado | 2.3.3 | [1,149] | biology, genomics, sequencing, pipeline |
MIKE | mike | 1.0 | [1,150] | geospatial, fluid_dynamics, modeling |
milvus | milvus | 2.4.15 | [1,151] | database, llm, container |
Minced | minced | 0.2.0 | [1,152] | biology, genomics |
Minia | minia | 3.2.6 | [1,153] | genomics, biology |
Miniasm | miniasm | 0.2-r168, 0.3-r179 | [1,154] | biology, phylogenetics |
MiniCaller | minicaller | 20161201 | [1,155] | biology, ngs, phylogenetics |
minigraph | minigraph | 0.15, 0.20 | [1,156] | phylogenetics |
minimac | minimac | 1-20130717, 3-20150727 | [1,157] | biology, genomics |
minimac2 | minimac | 2-20140915 | [1,158] | biology, ngs |
minimap | minimap | 2.21, 2.9-r720, 2.ax | [1,159] | biology, phylogenetics |
minimap2 | minimap2 | 2.24, 2.28 | [1,160] | genomics, biology |
Minipolish | minipolish | 0.1.3 | [1,161] | biology, genomics |
Miniprot | miniprot | 0.12 | [1,162] | biology, genomics |
miniwdl | miniwdl | 1.11.1 | [1,163] | bioinfomatics |
MinkowskiEngine | minkowskiengine | 0.5.3, 0.5.4a | [1,164] | machine_learning |
MinPath | minpath | 1.4 | [1,165] | biology, phylogenetics |
MIRA | mira | 4.0.rc1, 4.9.6, 5rc2 | [1,166] | biology, genomics, assembly |
miRanda | miranda | 1.9 | [1,167] | phylogenetics |
miRBShunter | mirbshunter | 0.2 | [1,168] | phylogenetics |
mirdeep | mirdeep | 0.1.0, 0.1.1, 2.0.1.3 | [1,169] | phylogenetics |
miRDP2 | mirdp2 | 1.1.4 | [1,170] | biology, genomics |
Mireap | mireap | 0.20 | [1,171] | biology |
miRge | mirge | 2.0 | [1,172] | phylogenetics |
Misa | misa | 1.0 | [1,173] | biology, genomics |
MISO | miso | 0.5.3 | [1,174] | biology, ngs, sequencing, rna-seq |
mistral | mistral | 0.1.5 | [1,175] | library, math |
MITE-Hunter | mite-hunter | 20111101 | [1,176] | biology, phylogenetics |
MITObim | mitobim | 1.9.1 | [1,177] | phylogenetics |
MitoFinder | mitofinder | 1.4.1 | [1,178] | phylogenetics |
mitohifi | mitohifi | 2.2, 3.2 | [1,179] | genomics, sequencing |
MitoPhAST | mitophast | 3.0 | [1,180] | phylogenetics |
Mitos | mitos | 2.1.9 | [1,181] | biology, phylogenetics |
Mitsuba2 | mitsuba2 | 2.2.1 | [1,182] | graphics |
MiXCR | mixcr | 2.1.8, 3.0.13 | [1,183] | biology, phylogenetics |
MixMHC2pred | mixmhc2pred | 1.2 | [1,184] | phylogenetics |
MixMHCpred | mixmhcpred | 2.0.2 | [1,185] | phylogenetics |
mixmogam | mixmogam | 20190322 | [1,186] | phylogenetics |
MKL | mkl | 2019.1.144, 2020.0.166, 2020.2.0 | [1,187] | programming, library, math, compiler |
mlcoalsim | mlcoalsim | 1.9916b | [1,188] | biology, phylogenetics |
mlpack | mlpack | 3.4.2 | [1,189] | library |
mlst | mlst | 2.15.2, 2.23.0 | [1,190] | phylogenetics |
mlstcheck | mlst-check | 2.1 | [1,191] | phylogenetics |
mmaction2 | mmaction2 | 1.0.0 | [1,192] | Machine_Learning, Visualization |
MMSEQ | mmseq | 1.0.8 | [1,193] | biology, genomics |
MMseqs2 | mmseqs2 | 11, 12, 14 | [1,194] | phylogenetics |
MMvec | mmvec | 1.0.5, 1.0.6 | [1,195] | metabolomics |
MNEtools | mnetools | 0.22.0, 1.3.1, 1.4.0 | [1,196] | phylogenetics |
MOABS | moabs | 1.2.9, 1.3.2, 1.3.4 | [1,197] | biology, ngs |
mobsuite | mobsuite | 3.1.0, 3.1.9 | [1,198] | sequencing, biology |
MOCCASIN | moccasin | 0.25 | [1,199] | phylogenetics |
moco | moco | 0.4.0 | [1,200] | modeling, tools |
Model Card Toolkit | model_card_toolkit | 2.0.0 | [1,201] | Machine_Learning, Utility, Workflow_automation |
MODELLER | modeller | 9.14, 9.23 | [1,202] | biology, modeling, structure |
MODELTEST | modeltest | 0.1.2, 0.1.7 | [1,203] | biology, phylogenetics |
ModernCSV | moderncsv | 2.0.2 | [1,204] | editor, viewer |
Modkit | modkit | 0.4.1 | [1,205] | genomics, bioinformatics |
Modulus | modulus | 23.11, 24.01, 24.07 | [1,206] | physics, ai, neural_network |
Molden | molden | 5.0, 7.3 | [1,207] | chemistry, structure |
molmim | molmim-nim | 1.0.0 | [1,208] | drug disovery, molecule generation |
MolPro | molpro | 0.1 | [1,209] | biology |
MolProbity | molprobity | 20221216 | [1,210] | biology |
momi | momi | 2.1.19 | [1,211] | phylogenetics, biology |
monai | monai | 0.8.1, 0.9.0, 1.0.1 | [1,212] | healthcare |
MONAI label | ngc-monailabel | 0.3.2, 0.6.0 | [1,213] | healthcare |
MongoDB | mongodb | 4.0.3 | [1,214] | database |
Moni | moni | 0.2.0 | [1,215] | genomics, biology |
mono | mono | 5.18 | [1,216] | linux, programming |
Monolix | monolix | 2023R1, 4.3.2 | [1,217] | modeling, biology |
MOOSE | moose | 20220610, 20230320, 20230711 | [1,218] | physics, simulation |
mopac | mopac | 22.1.1 | [1,219] | chemistry |
MORPHEUS | morpheus | 23.01 | [1,220] | machine_learning |
Mosaic | mosaic | 1.7.4 | [1,221] | phylogenetics |
MOSAIK | mosaik | 2.1.33, 2.2.3, 2.2.30 | [1,222] | biology, alignment |
Mosdepth | mosdepth | 0.2.3, 0.3.1 | [1,223] | biology, phylogenetics |
moses | moses | 0.3.1 | [1,224] | machine learning, data science |
Mothur | mothur | 1.41.3, 1.46.1, 1.48.0 | [1,225] | biology |
MotionCor2 | motioncor2 | 1.2.3, 1.3.1, 1.6.4 | [1,226] | imaging |
mOTU | motu | 1.1 | [1,227] | biology, genomics |
mOTUs | motus | 2.5.1 | [1,228] | phylogenetics |
MountainSort | mountainsort | 0.9.0 | [1,229] | library |
MP-EST | mpest | 1.4 | [1,230] | biology, ngs, sequencing |
MPACK | mpack | 0.8.0 | [1,231] | library |
MPB | mpb | 1.5 | [1,232] | library, math |
MPBoot | mpboot | 1.1.0 | [1,233] | biology, phylogenetics |
MPFR | mpfr | 3.1.6, 4.2.1 | [1,234] | library, math |
mpi-test-suite | mpi-test-suite | 1.1.1 | [1,235] | utility |
mpinterfaces | mpinterfaces | 20170613 | [1,236] | math |
MrBayes | mrbayes | 3.2.4, 3.2.5, 3.2.6 | [1,237] | biology, phylogenetics |
MRIcroGL | mricrogl | 20201102, 20210327, 20211006 | [1,238] | biology, imaging |
MRIcron | mricron | 201306, 20161012, 20190911 | [1,239] | biology, imaging |
mriqc | mriqc | 0.11.0, 0.16.1, 22.0.1 | [1,240] | mri, imaging, biology |
MRtrix | mrtrix | 3.0.1, 3.0.3, 3.0rc2 | [1,241] | biology, imaging |
mrtrix3tissue | mrtrix3tissue | 5.2.9 | [1,242] | phylogenetics |
ms | ms | 20171108 | [1,243] | phylogenetics |
ms-dial | ms-dial | 4.4.8 | [1,244] | biology, metabolomics |
msfinder | msfinder | 3.52 | [1,245] | biology, metabolomics |
mSINGS | msings | 20180810 | [1,246] | phylogenetics |
MSMC-Tools | msmc-tools | 20190614 | [1,247] | phylogenetics |
msprime | msprime | 0.7.4, 1.2.0 | [1,248] | phylogenetics |
MstatX | mstatx | 1.0 | [1,249] | biology, phylogenetics |
MSTmap | mstmap | 1.0 | [1,250] | phylogenetics |
msvar | msvar | 1.3 | [1,251] | biology, genomics |
MTG2 | mtg2 | 2.15 | [1,252] | phylogenetics |
mTR | mtr | 20210526, 20240801 | [1,253] | biology, genomics |
Mugsy | mugsy | 1.2.3 | [1,254] | biology, phylogenetics |
Multimatch-gaze | multimatchgaze | 0.1.3 | [1,255] | math, data_science |
MultiQC | multiqc | 1.21, 1.24, 1.7 | [1,256] | biology, ngs, sequencing |
MUMmer | mummer | 3.23, 4.0.0beta2 | [1,257] | biology, genomics |
MUSCLE | muscle | 3.8.31, 5.1 | [1,258] | biology, alignment |
MuSE | muse | 1.0rc | [1,259] | phylogenetics |
Musket | musket | 1.1 | [1,260] | biology, genomics, ngs |
MuTect | mutect | 1.1.4, 1.1.7 | [1,261] | biology, genomics |
mutmap | mutmap | 2.3.3 | [1,262] | biology |
MutSig | mutsig | 1.4, 1.41 | [1,263] | biology, genomics |
mvftools | mvftools | 20191124 | [1,264] | phylogenetics |
mvrsion | mvrsion | 07302018 | [1,265] | sequencing |
mxnet | ngc-mxnet | 22.08 | [1,266] | healthcare |
mykrobe | mykrobe | 0.12.2 | [1,267] | biology |
MZMine | mzmine | 2.53, 3.3.0 | [1,268] | biology, spectroscopy |
NAMD | namd | 2.14b2, 3.0 Alpha, 3.0b2 | [1,269] | molecular_dynamics |
NANO | nano | 2.8.2 | [1,270] | programming |
nanocaller | nanocaller | 3.1.0 | [1,271] | sequencing |
nanocomp | nanocomp | 1.17.0 | [1,272] | programming, sequencing |
Nanocompore | nanocompore | 1.3.0 | [1,273] | biology, genomics |
NanoCount | nanocount | 0.2.1 | [1,274] | phylogenetics |
Nanodisco | nanodisco | 1.0.3 | [1,275] | phylogenetics |
Nanofilt | nanofilt | 2.7.1 | [1,276] | phylogenetics |
nanolyse | nanolyse | 1.2.0 | [1,277] | genomics, biology |
NanoPlot | nanoplot | 1.30.1, 1.42.0 | [1,278] | phylogenetics |
Nanopolish | nanopolish | 0.11.1, 0.13.2, 20171006 | [1,279] | biology |
nanoq | nanoq | 0.10.0 | [1,280] | biology, ngs, nanopore |
nanostripper | nanostripper | 0.1 | [1,281] | phylogenetics, biology |
NanoSV | nanosv | 1.2.0, 1.2.3, 1.2.4 | [1,282] | biology, genomics |
NanoVar | nanovar | 1.3.9 | [1,283] | phylogenetics |
Napari | napari | 0.3.8, 0.4.7 | [1,284] | phylogenetics |
NBODY | nbody | 6 | [1,285] | astronomy |
NCBI BLAST+ | ncbi_blast | 2.7.1, 2.8.1, 2.9.0 | [1,286] | biology |
NCBI C++ Toolkit | ncbi_toolkit | 12.0.0, 21.0.0, 7.0.0 | [1,287] | biology, programming, library, compiler |
NCBI GenBank Tools | genbank_tools | 20140130 | [1,288] | biology |
ncbi-fcs | ncbi-fcs | 0.4.0, 0.5.0, 0.5.4 | [1,289] | genomics |
ncbi-genome-download | ncbi-genome-download | 0.3.3 | [1,290] | biology, genomics |
ncbi-vdb | ncbi-vdb | 2.6.3, 2.8.2 | [1,291] | ngs |
ncbi_cli | ncbi_cli | 15.3.1 | [1,292] | biology, sequencing, library |
nccl | nccl | 20.11 | [1,293] | programming, library, gpu |
ncftp | ncftp | 3.2.5 | [1,294] | file_management |
NCL | ncl | 6.1.2, 6.3.0, 6.6.2 | [1,295] | climate |
NCO | nco | 4.2.1, 4.4.3 | [1,296] | data_science |
ncview | ncview | 2.1.2, 2.1.7 | [1,297] | visualization |
NECAT | necat | 202001019, 20200803 | [1,298] | phylogenetics |
Necklace | necklace | 1.00 | [1,299] | biology, phylogenetics |
NeEstimator | neestimator | 2.1 | [1,300] | biology |
nemo | nemo | 1.2.0, 1.22.0, 1.23.0 | [1,301] | ai, machine_learning |
neovim | neovim | 0.8.1, 0.8.3, 0.9.5 | [1,302] | programming, shell |
nerfstudio | nerfstudio | 1.1.3 | [1,303] | Machine Learning |
NetCDF | netcdf | 4.3, 4.3.3, 4.4.3 | [1,304] | data_science |
NetCDF-C | netcdf-c | 4.8.1, 4.9.0, 4.9.2 | [1,305] | data_science |
NetCDF-F | netcdf-f | 4.5.3, 4.5.4, 4.6.1 | [1,306] | data_science |
NetLogo | netlogo | 5.3.64, 6.1.1, 6.2.0 | [1,307] | modeling |
NEURON | neuron | 7.7.2, 8.0.0, 8.2.1 | [1,308] | biology, neuroscience |
Newbler | newbler | 2.7, 2.8, 2.9 | [1,309] | biology, ngs, assembly, de_novo |
newick-utils | newickutils | 1.6 | [1,310] | biology, genomics, phylogenetics |
newick_utils | newick_utils | 1.6, 1.7 | [1,311] | biology, phylogenetics |
NewTargets | newtargets | 20210215 | [1,312] | biology |
nextclade | nextclade | 2.9.1, 3.2.0, 3.8.2 | [1,313] | phylogenetics, genomics |
NextDenovo | nextdenovo | 2.4.0 | [1,314] | phylogenetics |
Nextflow | nextflow | 23.10.0, 23.10.1, 24.04.2 | [1,315] | biology, workflow_automation |
NextGenMap | nextgenmap | 0.5.5 | [1,316] | phylogenetics |
NextPolish | nextpolish | 1.3.1 | [1,317] | phylogenetics |
Nextstrain | nextstrain | 1.16.1 | [1,318] | phylogenetics |
nf-core | nf-core | 2.11.1, 2.14.1, 2.7.2 | [1,319] | biology, workflow_automation |
NGC CLI | ngccli | 2.10.1 | [1,320] | shell |
NGmerge | ngmerge | 0.3 | [1,321] | phylogenetics |
ngmlr | ngmlr | 0.2.6, 0.2.7 | [1,322] | biology, phylogenetics |
ngs-bits | ngsbits | 0.1 | [1,323] | biology, sequencing |
NGS-SDK | ngs-sdk | 1.2.4, 1.3.0 | [1,324] | biology, healthcare, programming, library |
ngsremix | ngsremix | 20221117 | [1,325] | genomics |
ngstools | ngstools | 20150816 | [1,326] | biology, ngs |
nilearn | nilearn | 0.7.0, 0.9.0 | [1,327] | phylogenetics |
nimare | nimare | 0.0.5 | [1,328] | neuroscience |
Nipype | nipype | 1.6.0, 1.7.0, 1.8.0 | [1,329] | biology, neuroscience, imaging |
nlp | nlp | 1.1, 1.2, 1.3 | [1,330] | machine_learning |
nlr-annotator | nlr-annotator | 0.7 | [1,331] | phylogenetics |
NLR-Parser | nlr-parser | 1.0 | [1,332] | phylogenetics |
nlrtracker | nlrtracker | 20240306 | [1,333] | biology |
NMRPipe | nmrpipe | 7.9, 8.2 | [1,334] | chemistry, biology |
NONMEM | nonmem | 7.3.0, 7.4.4 | [1,335] | modeling |
nonpareil | nonpareil | 3.3.4 | [1,336] | phylogenetics |
Novoalign | novoalign | 2.08.02, 3.00.02 | [1,337] | biology, ngs |
NOVOPlasty | novoplasty | 3.7, 4.2, 4.3 | [1,338] | phylogenetics |
nPhase | nphase | 1.1.3 | [1,339] | biology, pipeline |
npScarf | japsa | 1.7 | [1,340] | phylogenetics |
nQuire | nquire | 20180405 | [1,341] | phylogenetics |
Nsight | nsight | 2022.1, 2024.3.2.0 | [1,342] | gpu, performance_analysis, utility |
Nsightsys | nsightsys | 2022.2.1, 2024.5.1 | [1,343] | gpu, performance_analysis, utility |
nt | nt | 20220404 | [1,344] | sequencing, neuroscience |
ntEdit | ntedit | 1.2.1 | [1,345] | phylogenetics |
ntJoin | ntjoin | 1.1.4 | [1,346] | biology, genomics |
nubeamdedup | nubeamdedup | 20200907 | [1,347] | phylogenetics |
NucDiff | nucdiff | 2.0.3 | [1,348] | phylogenetics |
NucleoATAC | nucleoatac | 0.3.1 | [1,349] | biology |
Nuke | nuke | 14.0v5 | [1,350] | Graphics, Utility, Visualization |
Nullarbor | nullarbor | 1.41 | [1,351] | biology, phylogenetics |
Numba | numba | 0.36.2, 0.43.1, 0.48.0 | [1,352] | compiler |
NUPACK | nupack | 3.2.2 | [1,353] | phylogenetics |
nvhpc | nvhpc | 23.7, 24.3, 24.5 | [1,354] | language, programming, library, math, gpu |
nvhpc_multi | nvhpc_multi | 23.5.multi | [1,355] | language, programming, library, math, gpu |
nVidia HPC Compilers | nvidia | 20.11 | [1,356] | compiler |
NWChem | nwchem | 6.8, 7.2, 7.2.3 | [1,357] | chemistry |
NxTrim | nxtrim | 0.4.1 | [1,358] | biology, ngs |
Oases | oases | 0.2.08 | [1,359] | biology, ngs, assembly |
Oatk | oatk | 1.0 | [1,360] | genomics |
Obitools | obitools | 1.2.13, 3.0 | [1,361] | biology, ngs, sequencing |
OCaml | ocaml | 4.02.3 | [1,362] | language, programming |
OCOCO | ococo | 0.1.2.6 | [1,363] | biology, phylogenetics |
octave | octave | 6.4.0, 7.2.0, 7.3.0 | [1,364] | math |
odgi | odgi | 0.6, 0.8.4 | [1,365] | phylogenetics |
Olego | olego | 1.1.2, 1.1.5, 1.1.6 | [1,366] | biology, ngs, rna-seq |
ollama | ollama | 0.3.8, 0.4.4 | [1,367] | LLM |
OMindel | omindel | 20180129 | [1,368] | phylogenetics |
OMNI-C | omnic | 1.0 | [1,369] | genomics |
omniCLIP | omniclip | 0.1.0 | [1,370] | phylogenetics |
OMNIVERSE | omniverse | beta211004 | [1,371] | gpu |
OMSV | omsv | 1.0.1 | [1,372] | phylogenetics |
OneFormer | oneformer | 1.0 | [1,373] | ai, image_processing, imaging |
ONT-Bonito | ont-bonito | 0.1.5, 0.5.3, 0.6.0 | [1,374] | phylogenetics |
ont_fast5_api | ont-fast5-api | 2.0.1, 4.0.2 | [1,375] | phylogenetics |
ont_tutorial_cas9 | ont_tutorial_cas9 | 20190705 | [1,376] | phylogenetics |
open-cravat | open-cravat | 2.0.1 | [1,377] | biology, genomics |
open3d | open3d | 0.13.0, 0.17.0 | [1,378] | graphics |
OPENACC | openacc | 16.7 | [1,379] | programming |
OpenBabel | openbabel | 2.3.2, 2.4.1, 3.1.1 | [1,380] | biology |
OpenBLAS | openblas | 0.2.20, 0.3.24 | [1,381] | programming, library |
OpenCL | opencl | 18.1.0.013 | [1,382] | phylogenetics |
OpenCV | opencv | 4.5.2, 4.7.0 | [1,383] | library |
OpenFOAM | openfoam | 4.1, 5.0, 8.0 | [1,384] | fluid_dynamics |
openmc | openmc | 0.14.0, 0.15.0 | [1,385] | physics |
OpenMM | openmm | 7.6.0, 8.0.0, 8.1.2 | [1,386] | chemistry, molecular_dynamics |
OpenMPI | openmpi | 4.1.4, 4.1.5, 4.1.6 | [1,387] | programming, library |
OpenNeuro | openneuro | 3.17.4, 3.37.4, 4.19.2 | [1,388] | biology, data_science |
opennmt-py | opennmt-py | 3.1.0 | [1,389] | language, machine_learning |
OpenPIV-python | openpiv | 0.21.2 | [1,390] | programming, imaging |
OpenPIV-python-gpu | openpiv | 20190506-gpu | [1,391] | programming, imaging |
OpenPose | openpose | 20230106 | [1,392] | image_processing |
openrdp | openrdp | 0.1.0-rc2 | [1,393] | biology |
opensim | opensim | 5.4 | [1,394] | biology, neuroscience, medicine, dynamic movments of musculoskeletal structures |
OpenSim | opensim | 4.3 | [1,395] | phylogenetics |
OpenSlide | openslide | 3.4.1 | [1,396] | imaging |
Openssl | openssl | 3.3.0, 3.4.0 | [1,397] | libray |
openstructure | openstructure | 2.3.1 | [1,398] | biology |
OpenUSD | openusd | 23.08 | [1,399] | digital twin, simulation |
OptiType | optitype | 1.3.1 | [1,400] | biology, phylogenetics |
Orange3 | orange3 | 3.3.6 | [1,401] | data_mining |
Orca | orca | 5.0.1, 5.0.4 | [1,402] | chemistry |
ORCA | orca | 4.0.1.2 | [1,403] | chemistry, structure |
OrganellePBA | organellepba | 20180904 | [1,404] | phylogenetics |
OrthoFiller | orthofiller | 1.1.4 | [1,405] | phylogenetics |
OrthoFinder | orthofinder | 2.3.11, 2.5.2, 2.5.5 | [1,406] | biology, ngs |
Orthofisher | orthofisher | 0.1.2 | [1,407] | biology, genomics |
Orthograph | orthograph | 0.6.3 | [1,408] | orthology |
Orthologer | orthologer | 2.2.0 | [1,409] | biology |
OrthoMCL | orthomcl | 2.0.9 | [1,410] | biology, genomics |
OSL | osl | 1.1.0 | [1,411] | biology, neuroscience, imaging |
oslom | oslom | 0.3.0 | [1,412] | plotting |
osprey | osprey | 1.1.0, 2.5.0 | [1,413] | spectroscopy, neuroscience |
OTB | otb | 5.8.0 | [1,414] | geospatial |
ovito | ovito | 3.8.5, 3.9.4 | [1,415] | programming |
owitools | owitools | 1.0 | [1,416] | metabarcoding, bioinformatics, ecology |
p4est | p4est | 1.1, 2.8 | [1,417] | library |
p4vasp | p4vasp | 0.3.29, 0.3.30 | [1,418] | visualization |
p53MH | p53mh | 20020901 | [1,419] | biology, sequencing |
p7zip | p7zip | 9.20.1 | [1,420] | utility |
PacBio | pacbio | 10.2.0.133434, 11.0.0.146107, 7.0.1 | [1,421] | biology, ngs |
Package-GFE | package-gfe | 20150701 | [1,422] | biology, genomics |
PacMAP | pacmap | 0.7.0 | [1,423] | genomics |
PALADIN | paladin | 1.3.1 | [1,424] | biology, phylogenetics |
PALES | pales | 122 | [1,425] | physics |
PAML | paml | 4.8a, 4.9a, 4.9h | [1,426] | biology, phylogenetics |
panaroo | panaroo | 1.3.3 | [1,427] | biology, genomics |
Pandaseq | pandaseq | 20140808, 20150627 | [1,428] | biology, ngs, sequencing |
Pandoc | pandoc | 2.2.2.1 | [1,429] | utility |
pangolin | pangolin | 2, 4.3 | [1,430] | phylogenetics |
PANPIPES | panpipes | 20240822 | [1,431] | biology |
panseq | panseq | 3.2.1 | [1,432] | phylogenetics |
pantools | pantools | 4.3.1 | [1,433] | biology, genomics |
panX | panx | 1.6.0 | [1,434] | phylogenetics |
PAPI | papi | 5.5.1, 5.7.0 | [1,435] | programming, performance_analysis |
parabricks | parabricks | 4.2.1, 4.3.0, 4.3.1 | [1,436] | phylogenetics |
parallel | parallel | 20150122, 20170322 | [1,437] | shell, workflow_automation |
paralyzer | paralyzer | 1.5 | [1,438] | phylogenetics |
ParaView | paraview | 5.4.1, 5.7.0, 5.9.1.1 | [1,439] | data_science |
ParaView Server | paraview_server | 5.10.1 | [1,440] | data_science |
ParGenes | pargenes | 1.2.0 | [1,441] | phylogenetics |
ParlAI | parlai | 1.3.0, 1.5.0 | [1,442] | phylogenetics |
PARMETIS | parmetis | 4.0.3 | [1,443] | utility |
Parsnp | parsnp | 1.2, 1.5.0, 1.6.2 | [1,444] | biology, phylogenetics |
PartitionFinder | partitionfinder | 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 | [1,445] | biology, phylogenetics, genomics |
PASA | pasa | 2.2.0-r20171013, 2.4.1, 2.5.3 | [1,446] | biology, genomics, ngs |
Pascal | fpc | 3.0.0 | [1,447] | compiler, programming |
PASTA | pasta | 0.2.0, 1.7.8, 20160616 | [1,448] | biology, alignment |
PATHd8 | pathd8 | 1.0 | [1,449] | biology, phylogenetics |
pathoscope | pathoscope | 2.0.7 | [1,450] | sequencing, genomics, biology |
PATRIC | patric | 1.034 | [1,451] | machine_learning |
PAUDA | pauda | 1.0.1 | [1,452] | biology, ngs, phylogenetics |
PAUP | paup | 4.0a166, 4.0a168, 4.0b10 | [1,453] | biology, phylogenetics |
PB-Assembly | pb-assembly | 0.0.6, 0.0.8 | [1,454] | biology, ngs, sequencing |
pbalign | pbalign | 20160921, 20161221 | [1,455] | biology |
PBCCS | pbccs | 5.0.0, 6.4.0 | [1,456] | phylogenetics |
pbcore | pbcore | 1.7.1 | [1,457] | biology |
PBGCpp | pbgcpp | 1.9.0 | [1,458] | phylogenetics |
pbipa | pbipa | 1.8.0 | [1,459] | phylogenetics, biology |
PBJelly | pbjelly | 15.8.24 | [1,460] | biology, ngs |
pbmm2 | pbmm2 | 1.13.1, 1.3.0 | [1,461] | phylogenetics |
pbpigeon | pbpigeon | 1.2.0 | [1,462] | biology, ngs |
pbrt | pbrt | 20181017 | [1,463] | phylogenetics |
pbsmrtpipe | pbsmrtpipe | 0.63.0 | [1,464] | biology, programming |
pbtk | pbtk | 3.1.0 | [1,465] | biology |
pbtranscript-tofu | pbtranscript-tofu | 20150317, 20160119 | [1,466] | biology, ngs |
pcangsd | pcangsd | 1.2 | [1,467] | biology |
PCIT | pcit | 2014 | [1,468] | biology |
PCRE | pcre | 8.38, 8.39 | [1,469] | programming, library |
PDA | pda | 1.0.3 | [1,470] | biology, phylogenetics |
pdb2pqr | pdb2pqr | 2.1.0 | [1,471] | protein, modeling, biology |
PeakSplitter | peaksplitter | 1.0 | [1,472] | biology, chip-seq |
PEAR | pear | 0.9.2 | [1,473] | biology, genomics, ngs |
peneasy | peneasy | 20150530 | [1,474] | physics |
PennCNV | penncnv | 1.0.5 | [1,475] | phylogenetics |
Perl | perl | 5.16.0, 5.20.0, 5.24.1 | [1,476] | programming, language |
PerM | perm | 0.4.0 | [1,477] | biology, ngs, mapping |
PETSc | petsc | 3.8.1, 3.8.3, 3.8.4 | [1,478] | math |
PfamScan | pfamscan | 1.3, 1.5 | [1,479] | biology, genomics |
PGAP | pgap | 20230306, 20231003, 20240703 | [1,480] | biology, genomics, annotation, pipeline |
PGDSpider | pgdspider | 2.0.9.0, 2.1.1.5 | [1,481] | biology, ngs |
pggb | pggb | 0.6.0, 20201106, 20210121 | [1,482] | phylogenetics |
PhaME | phame | 1.0.3 | [1,483] | phylogenetics |
phanotate | phanotate | 1.5.0 | [1,484] | genomics |
pharmcat | pharmcat | 1.8.0 | [1,485] | biology, phylogenetics |
PHASE | phase | 2.1.1 | [1,486] | phylogenetics |
PHAST | phast | 1.5 | [1,487] | biology, phylogenetics |
Phenix | phenix | 1.10.2155, 1.17.1, 1.8.1069 | [1,488] | material_science |
PHI | phi | 3.1.1, 3.1.2b, 3.1.6 | [1,489] | math |
PhiSpy | phispy | 3.2 | [1,490] | phylogenetics |
PHLAWD | phlawd | 20170427 | [1,491] | biology, phylogenetics |
PhotoScan | photoscan-pro | 1.4.1, 1.4.5 | [1,492] | image_processing |
Photutils | photutils | 0.5 | [1,493] | astronomy |
PHYling | phyling | 1.0 | [1,494] | biology, phylogenetics, genomics |
PHYLIP | phylip | 3.696 | [1,495] | biology, phylogenetics |
PhyloAcc | phyloacc | 1.0 | [1,496] | phylogenetics |
PhyloBayes | phylobayes | 3.3f | [1,497] | biology, phylogenetics |
phyloFlash | phyloflash | 3.3b4 | [1,498] | phylogenetics |
phylonet | phylonet | 3.5.7, 3.8.2 | [1,499] | biology, phylogenetics |
PhyloParser | phyloparser | 20180404 | [1,500] | phylogenetics |
PhyloPhlAn2 | phylophlan2 | 0.41 | [1,501] | phylogenetics |
phylopypruner | phylopypruner | 1.2.3 | [1,502] | phylogenetics |
PhyloSift | phylosift | 1.1 | [1,503] | biology, genomics, phylogenetics |
phyloTF2 | phylotf2 | 20210726 | [1,504] | biology, genomics, alignment |
Phyluce | phyluce | 20180727, 20190308, 20191015 | [1,505] | biology, ngs, sequencing |
PhyML | phyml | 3.0, 3.1, 3.3.20220408 | [1,506] | biology, phylogenetics |
phynd | phynd | 20200409 | [1,507] | phylogenetics |
Physher | physher | 1.0.2 | [1,508] | phylogenetics |
PHYUTILITY | phyutility | 2.7.1 | [1,509] | biology |
Phyx | phyx | 1.1 | [1,510] | phylogenetics |
PIA2 | pia2 | 20180305 | [1,511] | biology, phylogenetics |
Picard-tools | picard | 2.9.2, 3.1.1, 3.2.0 | [1,512] | biology, ngs |
PICRUSt | picrust | 1.1.3, 1.1.4, 2.3.0b | [1,513] | biology, phylogenetics |
PICSL | picsl | 1.3 | [1,514] | imaging |
Piggy | piggy | 20171220 | [1,515] | biology, ngs |
Pigz | pigz | 2.4 | [1,516] | compression |
PILON | pilon | 1.22, 1.24 | [1,517] | biology, ngs, phylogenetics |
Pindel | pindel | 0.2.5b8 | [1,518] | biology, phylogenetics |
pipe-clip | pipe-clip | 1.1.0 | [1,519] | biology, ngs |
pipits | pipits | 1.3.6, 1.4.0 | [1,520] | biology, sequencing |
Piranha | piranha | 1.2.1 | [1,521] | biology, phylogenetics |
PLantismash | plantismash | 1.0 | [1,522] | biology, genomics |
PlantTribes | planttribes | 1.0.4 | [1,523] | phylogenetics |
plasme | plasme | 1.1 | [1,524] | Genomics |
PLAST | plast | 1.0, 2.3.2 | [1,525] | biology |
platanus | platanus | 1.2.4 | [1,526] | phylogenetics |
Platon | platon | 1.6 | [1,527] | biology, sequencing |
Platypus | platypus | 0.8.1 | [1,528] | biology, ngs |
PLEK | plek | 1.2.2 | [1,529] | biology, phylogenetics |
Plink | plink | 2.00a2, 2.00a3LM, 2.00a5LM | [1,530] | biology, genomics, phylogenetics |
plinkseq | plinkseq | 0.10 | [1,531] | biology, library |
plip | plip | 2.3.0 | [1,532] | Protein-structure |
plotsr | plotsr | 0.5.4 | [1,533] | genomics, biology |
PLUMED | plumed | 2.7.3, 2.9.0, 2021.2 | [1,534] | chemistry, molecular_dynamics |
pm4py | pm4py | 2.7.4 | [1,535] | Data_Mining, Machine_Learning |
pod5 | pod5 | 0.1.5, 0.3.6, 20220621 | [1,536] | sequencing |
PolyGembler | polygembler | 1.0 | [1,537] | phylogenetics |
PolyPHen | polyphen | 2.2.2.r405b | [1,538] | biology, genomics |
polyply | polyply | 1.3.0 | [1,539] | phylogenetics, biology |
Polypolish | polypolish | 0.5.0 | [1,540] | biology, genomics |
pomdp | pomdp | 1.3.4 | [1,541] | software |
pomoxis | pomoxis | 0.1.11, 0.2.5, 0.3.2 | [1,542] | biology, phylogenetics |
popcorn | popcorn | 20211104 | [1,543] | phylogenetics, biology |
PopLDdecay | poplddecay | 3.40 | [1,544] | phylogenetics |
popoolation | popoolation | 1.2.2 | [1,545] | biology, phylogenetics |
popoolation2 | popoolation2 | 1.201 | [1,546] | biology, phylogenetics |
Porechop | porechop | 0.2.4 | [1,547] | phylogenetics |
Poretools | poretools | 0.6.1 | [1,548] | phylogenetics |
portcullis | portcullis | 1.2.3 | [1,549] | phylogenetics |
PosiGene | posigene | 20171113 | [1,550] | biology, phylogenetics |
POV-Ray | povray | 3.7, 3.7.0.8 | [1,551] | graphics |
powerfit | powerfit | 2.0.0 | [1,552] | Physics |
pplacer | pplacer | 1.1.alpha19 | [1,553] | biology, phylogenetics, genomics |
PRANK | prank | 170427, 20150803 | [1,554] | biology, alignment |
Predector | predector | 20201110 | [1,555] | phylogenetics |
predectorutils | predectorutils | 0.9.1 | [1,556] | biology, genomics |
preplot | preplot | 14.0.2 | [] | |
Preseq | preseq | 0.0.4 | [1,557] | biology, ngs |
PRICE | price | 1.2 | [1,558] | biology, ngs |
Primer3 | primer3 | 2.3.4 | [1,559] | biology, genomics |
primus | primus | 1.8.0 | [1,560] | biology, phylogenetics |
PRINSEQ | prinseq | 0.20.4 | [1,561] | biology, sequencing |
PRINSEQ++ | prinseq++ | 1.2 | [1,562] | phylogenetics |
ProbABEL | probabel | 0.4.2, 0.4.3, 0.4.5 | [1,563] | genomics |
probalign | probalign | 1.4 | [1,564] | biology, ngs |
Processing | processing | 3.4 | [1,565] | programming, language, visualization |
Prodigal | prodigal | 2.6.2, 2.6.3 | [1,566] | biology, genomics |
ProDy | prody | 2.0 | [1,567] | phylogenetics |
Program Database Toolkit | pdt | 3.20, 3.22, 3.24 | [1,568] | language, programming, performance_analysis |
PROJ | proj | 5.1.0, 8.0.1, 9.4.0 | [1,569] | library, Cartographic Projections and Coordinate Transformations |
Prokka | prokka | 1.12, 1.14.6 | [1,570] | biology, genomics, assembly |
Proovread | proovread | 1.03rcl, 2.12, 2.13 | [1,571] | biology, genomics, ngs |
ProSplign | prosplign | 1.0.0 | [1,572] | phylogenetics |
Protege | protege | 5.1.0 | [1,573] | genomics |
Proteinortho | proteinortho | 4.26, 5.11, 5.16 | [1,574] | biology, genomics |
ProtExcluder | protexcluder | 1.2 | [1,575] | biology, phylogenetics |
ProtHint | prothint | 2.6.0 | [1,576] | biology, genomics |
protobuf | protobuf | 2.5.0, 3.5.1 | [1,577] | web, library |
prottest3 | prottest3 | 3.4.2 | [1,578] | biology |
PROVEAN | provean | 1.1.5 | [1,579] | biology, genomics |
PRSice | prsice | 2.3.3 | [1,580] | phylogenetics |
Pseudofinder | pseudofinder | 1.0 | [1,581] | phylogenetics |
PsiCLASS | psiclass | 1.0.1 | [1,582] | phylogenetics |
PSMC | psmc | 0.6.5 | [1,583] | phylogenetics |
psRobot | psrobot | 1.2 | [1,584] | phylogenetics |
Pufferfish | pufferfish | 20200417, 20230223 | [1,585] | phylogenetics |
PureCLIP | pureclip | 1.1.1 | [1,586] | phylogenetics |
Purge_Dups | purge_dups | 1.0.1 | [1,587] | phylogenetics |
purge_haplotigs | purge_haplotigs | 1.1.2, 1.1.3 | [1,588] | sequencing, biology |
pvconv | pvconv | 10152018 | [1,589] | imaging |
pyani | pyani | 0.2.10, 0.2.12 | [1,590] | phylogenetics |
Pybedtools | pybedtools | 0.8.2, 0.9.0 | [1,591] | phylogenetics |
Pybind11 | pybind11 | 2.13.5 | [1,592] | programming |
PyBSASeq | pybsaseq | 20200623 | [1,593] | phylogenetics |
PyCharm | pycharm | 2018.3, 2023.1.2 | [1,594] | programming |
Pycharm Pro | pycharm-pro | 23.1.3 | [1,595] | software |
pychopper | pychopper | 2.5.0, 2.7.1 | [1,596] | phylogenetics, sequencing |
PyCogent | pycogent | 1.9 | [1,597] | biology, genomics |
pycoqc | pycoqc | 2.5.2 | [1,598] | sequencing |
PyCUDA | pycuda | 2024.1 | [1,599] | GPU programming |
pydarwin | pydarwin | 3.0.0 | [1,600] | machine_learning |
PyDeface | pydeface | 2.0.0 | [1,601] | imaging |
pydock3 | pydock3 | 20240513 | [1,602] | biology |
pyEGA3 | pyega3 | 3.4.1, 5.0.2 | [1,603] | biology, genomics, utility |
PyEXR | pyexr | 0.3.10 | [1,604] | programming |
Pyfaidx | pyfaidx | 0.5.2 | [1,605] | biology, ngs, sequencing |
pyfasta | pyfasta | 0.5.2 | [1,606] | phylogenetics |
pyfastx | pyfastx | 2.1.0 | [1,607] | bioinformatics |
PyG | ngc-pyg | 24.11D3.0 | [1,608] | library, math |
pygenometracks | pygenometracks | 3.8 | [1,609] | genomics, biology |
pygot | pygot | 20170518 | [1,610] | biology, phylogenetics |
pyhdf | pyhdf | 0.9.0 | [1,611] | library |
PyHIST | pyhist | 1.0 | [1,612] | biology, imaging, image_processing |
pymesh | pymesh | 0.3.0 | [1,613] | math, graphics |
pypaftol | pypaftol | 1.0 | [1,614] | biology, ngs, phylogenetics |
PyPHLAWD | pyphlawd | 20180416, 20190414 | [1,615] | biology, phylogenetics |
Pyroms | pyroms | 1.0 | [1,616] | geospatial |
PyRosetta | pyrosetta | r56324 | [1,617] | biology, structure, modeling |
pyrpipe | pyrpipe | 0.0.3 | [1,618] | phylogenetics |
Pysamstats | pysamstats | 1.1.2 | [1,619] | phylogenetics |
PySLURM | pyslurm | 18.08.04 | [1,620] | scheduler |
Python | python | 3.6.3, 3.6.5, 3.8 | [1,621] | programming, language |
Python-core | python-core | 3.6.5, 3.7, 3.8 | [1,622] | language, programming |
Python2 | python | 2.7.11 | [1,623] | language, programming |
PyTorch | ngc-pytorch | 1.9.0, 2.3.0, 2.5.0 | [1,624] | library, math |
pytorch | pytorch | 1.9.0, 2.0.1, 2.2.0 | [1,625] | library, math |
Pytorch Lightning | pytorch_lightning | 2.2.0 | [1,626] | library, math |
PyVCF | pyvcf | 0.6.0, 0.6.8 | [1,627] | biology, phylogenetics |
PyVista | pyvista | 0.26.1 | [1,628] | phylogenetics |
pyweka | pyweka | 0.3.18 | [1,629] | phylogenetics |
QAPA | qapa | 1.3.1, 1.3.3 | [1,630] | phylogenetics |
qcat | qcat | 1.1.0 | [1,631] | phylogenetics |
qctool | qctool | 2.0.1 | [1,632] | phylogenetics |
qcustomplot-pyqt5 | qcustomplot-pyqt5 | 2.1.1.2 | [1,633] | plotting, visualization |
QD | qd | 2.3.22 | [1,634] | library, compiler, math |
QDD | qdd | 3.1.2 | [1,635] | biology, genomics, ngs |
QGIS | qgis | 2.18.0, 3.14.0 | [1,636] | geospatial |
QIIME2 | qiime2 | 2024.10, 2024.2, 2024.5 | [1,637] | biology, bioinformatics, metagenomics |
QMCPACK | qmcpack | 3.4.0 | [1,638] | library |
QRNA | qrna | 2.0.4 | [1,639] | phylogenetics |
qsirep | qsiprep | 0.19.1 | [1,640] | data_mining |
QT | qt | 5.15.4, 5.15.9, 6.7.3 | [1,641] | library |
QT5 | qt | 5.15.16 | [1,642] | library |
QTL-seq | qtl-seq | 2.2.2 | [1,643] | biology, sequencing, pipeline |
QTLtools | qtltools | 1.2, 1.3.1 | [1,644] | phylogenetics |
Quake | quake | 0.3 | [1,645] | biology, sequencing |
QualiMap | qualimap | 2.1.2, 2.3 | [1,646] | biology, sequencing, alignment |
Quantas | quantas | 1.0.4, 1.0.8, 1.0.9 | [1,647] | biology, ngs |
quantisnp | quantisnp | 2 | [1,648] | biology, genomics |
QuantLib | quantlib | 1.34 | [1,649] | financial, quantitative analysis |
quarTeT | quartet | 1.1.6 | [1,650] | phylogenetics |
QuartetScores | quartetscores | 1.0.0 | [1,651] | phylogenetics |
QUARTO | quarto | 1.4.550 | [1,652] | desktop publishing |
QUAST | quast | 5.0.0, 5.0.2, 5.2.0 | [1,653] | biology, ngs, sequencing, rna-seq |
quickmerge | quickmerge | 0.3 | [1,654] | phylogenetics |
Quickquartet | quickquartet | 1.0.0 | [1,655] | biology, ngs |
QUIP | quip | 20201029, 20210626 | [1,656] | phylogenetics |
QuorUM | quorum | 1.0.0 | [1,657] | biology |
qupath | qupath | 0.4.3 | [1,658] | biology, Imaging |
R | R | 4.2, 4.3, 4.4 | [1,659] | statistics |
r-index | r-index | 20190711 | [1,660] | phylogenetics |
r8s | r8s | 1.8, 1.81 | [1,661] | phylogenetics |
RACA | raca | 0.9.1.1 | [1,662] | biology, ngs |
Racon | racon | 1.4.10, 1.4.13, 1.5.0 | [1,663] | phylogenetics |
RADICAL | radical | 0.2 | [1,664] | biology, genomics |
radinitio | radinitio | 1.2.3 | [1,665] | biology |
radorgminer | radorgminer | 0.9 | [1,666] | genomics, biology, sequencing |
RaGOO | ragoo | 1.11 | [1,667] | phylogenetics |
Ragout | ragout | 2.3 | [1,668] | genomics |
RagTag | ragtag | 1.0.0, 2.0.1 | [1,669] | phylogenetics |
rainbow | rainbow | 2.0.4 | [1,670] | biology, sequencing |
Rainbowfish | rainbowfish | 0.1.0 | [1,671] | phylogenetics |
RAiSD | raisd | 2.8, 3.1 | [1,672] | phylogenetics |
Randfold | randfold | 2.0.1 | [1,673] | biology, RNA |
ranger | ranger | 1.9.3 | [1,674] | file_management |
Rapidnj | rapidnj | 2.3.3 | [1,675] | biology, phylogenetics |
Rapids Base | rapidsai | 24.02, 24.08 | [1,676] | data_science |
rapidsai | rapidsai | 23.02, 23.06, 24.04 | [1,677] | data_science |
rapidtide | rapidtide | 1.9.0 | [1,678] | phylogenetics |
RAPSearch | rapsearch | 2.24 | [1,679] | biology, phylogenetics |
RAPT | rapt | 0.5.5 | [1,680] | biology,assembly |
Rascaf | rascaf | 1.0.2 | [1,681] | biology |
Rasterio | rasterio | 1.3.10 | [1,682] | geospatial |
RATTLE | rattle | 1.0 | [1,683] | Sequencing |
RAVE | rave | 2.1 | [1,684] | biology, phylogenetics |
Raven | raven | 1.8.1 | [1,685] | assembly |
RawHash | rawhash | 2.1 | [1,686] | data, hashing, performance |
RAxML | raxml | 8.2.10, 8.2.12, 8.2.8 | [1,687] | biology, phylogenetics |
RAxML-NG | raxml-ng | 0.9.0, 1.0.2, 1.1.0 | [1,688] | phylogenetics |
razers3 | razers3 | 3.5.7 | [1,689] | biology, phylogenetics |
rbp-maps | rbp-maps | 0.1.4 | [1,690] | phylogenetics |
rcapptests | rcapptests | 1.0 | [1,691] | software |
rclone | rclone | 1.57.0, 1.58.1, 1.65.2 | [1,692] | web |
Rcorrector | rcorrector | 1.0.4 | [1,693] | phylogenetics |
RDKit | rdkit | 2020092, 2024092 | [1,694] | chemistry |
rDnaTools | rdnatools | 0.1.3 | [1,695] | phylogenetics |
read2tree | read2tree | 0.1.5 | [1,696] | alignment, biology, genomics, phylogenetics |
READemption | reademption | 1.0.0 | [1,697] | phylogenetics |
REAPR | reapr | 1.0.18 | [1,698] | biology, assembly |
Rebaler | rebaler | 0.2.0 | [1,699] | phylogenetics |
reCOGnizer | recognizer | 1.3.3 | [1,700] | phylogenetics |
recon | recon | 1.08 | [1,701] | biology, sequencing |
recycler | recycler | 0.7 | [1,702] | biology, sequencing |
Redis | redis | 2.8.13, 2.8.19 | [1,703] | database, data_science |
REDItools2 | reditools2 | 20200701 | [1,704] | phylogenetics |
Redundans | redundans | 0.14a | [1,705] | biology, phylogenetics |
refmaker | refmaker | 1.0 | [1,706] | biology, phylogenomics |
ReFrame | reframe | 3.2 | [1,707] | performance_analysis, utility |
regtools | regtools | 0.5.2 | [1,708] | biology, rna-seq, genomics |
release | release | 12082021 | [1,709] | molecular_dynamics, machine_learning |
ReLERNN | relernn | 1.0.0 | [1,710] | biology/AI |
RELION | relion | 4.0.1, 4.0.2, 5.0.0 | [1,711] | biology, imaging |
RelocaTE2 | relocate2 | 2.0.1 | [1,712] | phylogenetics |
REMORA | remora | 1.8.3, 1.8.5, 2.0.0 | [1,713] | performance_analysis |
REPdenovo | repdenovo | 20170222 | [1,714] | biology, phylogenetics |
RepeatAnalysis | repeatanalysis | 0.10.0, 0.12.2 | [] | biology, phylogenetics |
RepeatAnalysisTools | repeatanalysistools | 20210506 | [1,715] | biology, genomics, sequencing, utility |
RepeatExplorer | repeatexplorer | 20150506, 20180517 | [1,716] | biology, ngs |
RepeatMasker | repeatmasker | 4.0.9, 4.1.1, 4.1.7 | [1,717] | biology |
RepeatModeler | repeatmodeler | 1.0.8, 2.0 | [1,718] | biology |
repeatscout | repeatscout | 1.0.5 | [1,719] | biology |
RepeatSeq | repeatseq | 0.8.2 | [1,720] | phylogenetics |
reptile | reptile | 1.1 | [1,721] | biology, ngs, math |
ResFinder | resfinder | 4.0 | [1,722] | biology, genomics |
resistify | resistify | 0.1.0 | [1,723] | biology, molecular |
Resistome | resistome | 20170111 | [1,724] | phylogenetics |
Resolve | resolve | 18.1.4 | [1,725] | Graphics, Utility, Visualization |
RevBayes | revbayes | 1.0.9, 1.1.1, 1.2.3 | [1,726] | biology, phylogenetics |
RFAA | rfaa | 20240323 | [1,727] | biology, genomics |
RFMIX | rfmix | 2.03 | [1,728] | phylogenetics |
RGAugury | rgaugury | 2.2 | [1,729] | sequencing, biology |
RGI | rgi | 4.2.2, 5.1.1, 6.0.2 | [1,730] | phylogenetics |
RGIS | rgis | 20180211, 20180814 | [1,731] | geospatial |
RHash | rhash | 1.3.3 | [1,732] | programming |
RiboCode | ribocode | 1.2.11 | [1,733] | phylogenetics |
ribodetector | ribodetector | 0.3.1 | [1,734] | biology |
riboPicker | ribopicker | 0.4.3 | [1,735] | biology, sequencing |
RiboTaper | ribotaper | 1.3.1a | [1,736] | phylogenetics |
Ribotricer | ribotricer | 1.3.3 | [1,737] | phylogenetics |
RIGERJ | rigerj | 2.0.2 | [1,738] | phylogenetics |
rMATS turbo | rmats-turbo | 4.1.2 | [1,739] | biology, sequencing, genomics |
rmats2sashimiplot | rmats2sashimiplot | 2.0.3, 2.0.4 | [1,740] | phylogenetics |
Rmpi | Rmpi | 3.5.1, 4.0.3 | [1,741] | statistics, programming |
rnabloom | rnabloom | 2.0.1 | [1,742] | biology, ngs, sequencing, rna-seq |
rnaeditingindexer | rnaeditingindexer | 12152022 | [1,743] | data_mining |
RNAFramework | rnaframework | 2.7.2 | [1,744] | biology, RNA, sequencing |
RNAhybrid | rnahybrid | 2.1.1 | [1,745] | biology, genomics |
rnalysis | rnalysis | 3.7.0 | [1,746] | sequencing, biology |
RNAmmer | rnammer | 1.2 | [1,747] | biology, rna-seq |
rnaQUAST | rnaquast | 1.5.1 | [1,748] | biology, ngs, sequencing, rna-seq |
RNAsalsa | rnasalsa | 0.8.1 | [1,749] | biology, phylogenetics |
rnaseqlib | rnaseqlib | 20150721 | [1,750] | biology, phylogenetics, rna-seq |
RNAstructure | rnastructure | 6.3 | [1,751] | biology, sequencing |
Roary | roary | 3.12.0, 3.13.0, 3.4.1 | [1,752] | biology, genomics |
roguenarok | roguenarok | 20230418 | [1,753] | phylogenetics |
ROOT | root | 5.34.17, 6.0, 6.06.02 | [1,754] | data_science |
ROOTPy | rootpy | 20160323 | [1,755] | data_science |
Rosetta | rosetta | 2019.35.60890, 2021.16.61629, 2023.11.30 | [1,756] | biology, structure, modeling |
RoseTTAFold | rosettafold | 1.0.0 | [1,757] | phylogenetics |
rrnaselector | rrnaselector | 1.0 | [1,758] | biology, sequencing |
RSEG | rseg | 0.4.8 | [1,759] | biology, genomics |
RSEM | rsem | 1.2.31, 1.2.7, 1.3.3 | [1,760] | biology, ngs, sequencing |
RSeQC | rseqc | 2.6.4, 3.0.0, 5.0.3 | [1,761] | biology, ngs, rna-seq |
RStudio | rstudio | 1.4, 2021.09.0, 2022.02.3 | [1,762] | statistics |
rsync | rsync | 3.2.7 | [1,763] | software, utility |
RTGTools | rtgtools | 3.7.1 | [1,764] | biology, ngs |
Ruby | ruby | 2.5.1 | [1,765] | programming, language |
run_dbcan | run_dbcan | 4.0.0, 4.1.4 | [1,766] | biology |
Rust | rust | 1.62.1, 1.70.0, 1.76.0 | [1,767] | programming |
rvtests | rvtests | 2.1.0 | [1,768] | genomics, biology, sequencing |
S.A.G.E | s.a.g.e | 6.4.2 | [1,769] | phylogenetics |
Sabre | sabre | 1.0 | [1,770] | phylogenetics |
saffrontree | saffrontree | 0.1.2 | [1,771] | phylogenetics |
saige | saige | 0.45.0 | [1,772] | genomics |
Sailfish | sailfish | 0.6.3 | [1,773] | biology, genomics, ngs, rna-seq |
Salmon | salmon | 1.5.2, 1.8.0, 1.9.0 | [1,774] | biology, rna-seq |
SALSA | salsa | 20171009, 20191001, 20220408 | [1,775] | biology, ngs |
samapi | samapi | 0.4.0 | [1,776] | Imaging |
Sambamba | sambamba | 0.6.3, 0.6.6, 0.6.9 | [1,777] | biology, ngs |
samblaster | samblaster | 0.1.14, 0.1.24 | [1,778] | biology, ngs, sequencing |
sampledock | sampledock | 0.5.1 | [1,779] | molecular_dynamics, AI |
SAMStat | samstat | 1.08 | [1,780] | biology, ngs, sequencing |
Samtools | samtools | 1.7, 1.8, 1.9 | [1,781] | biology, ngs, sequencing |
SAS | sas | 9.4.8 | [1,782] | statistics, data_science |
Sate | sate | 2.2.7 | [1,783] | biology, phylogenetics |
Satsuma | satsuma | 3.0 | [1,784] | phylogenetics |
Satsuma2 | satsuma2 | 20161123, 3.1 | [1,785] | phylogenetics |
sc-im | scim | 0.8.2 | [1,786] | utility, visualization |
Scala | scala | 2.11.5, 3.0.1 | [1,787] | programming, language |
Scalablast | scalablast | 2.4.53 | [1,788] | biology, genomics |
ScaLAPACK | scalapack | 2.1.0, 2.2.0, 2.2.1.5 | [1,789] | programming, library |
scallop | scallop | 0.10.5 | [1,790] | phylogenetics |
Scalpel | scalpel | 0.1.1, 0.5.3 | [1,791] | biology, ngs |
scanpy | scanpy | 1.8.2 | [1,792] | biology |
scapp | scapp | 0.1.4 | [1,793] | genomics, assembly |
scGPT | scgpt | 0.1.2 | [1,794] | Biology, Data_Science, Genomics |
Schrodinger Maestro | maestro | 2024-1 | [1,795] | chemistry, molecular_dynamics |
Schrodinger Suite | schrodinger | 2023-2, 2023-3, 2024-2 | [1,796] | chemistry, molecular_dynamics |
sciann | sciann | 0.7.0.1 | [1,797] | machine_learning |
scikit-learn | scikit-learn | 1.4.1.post1 | [1,798] | Data_Science |
scipion | scipion | 3.0.0, 3.1.0 | [1,799] | image_processing |
Scipion | scipion | 1.2 | [1,800] | image_processing |
SCIrun | scirun | 5.0.Z | [1,801] | phylogenetics |
scnic | scnic | 1.0 | [1,802] | library |
Scoary | scoary | 1.6.16 | [1,803] | phylogenetics |
Scons | scons | 2.5.1, 3.1.2 | [1,804] | programming |
SCOP | scop | 20180311 | [1,805] | biology, assembly |
score-sde | score-sde | 20221110 | [1,806] | Machine_Learning |
Scrappie | scrappie | 1.4.2 | [1,807] | biology, genomics |
SCRATCH-1D | scratch1d | 1.0, 1.2, 2.0 | [1,808] | biology, ngs |
Screen | screen | 4.8.0, 4.9.1 | [1,809] | programming, shell |
SCRIPTURE | scripture | 20101211 | [1,810] | biology, genomics |
scVelo | scvelo | 0.2.5 | [1,811] | biology |
Scythe | scythe | 0.991 | [1,812] | biology, ngs |
sdsl | sdsl | 2.1.1 | [1,813] | library, compiler |
SE-MEI | se-mei | 0.1.0 | [1,814] | phylogenetics |
SeCaPr | secapr | 1.1.12, 2.0.2, 2.1.1 | [1,815] | phylogenetics |
seekdeep | seekdeep | 3.0.1 | [1,816] | biology, sequencing |
Segemehl | segemehl | 0.1.9, 0.3.4 | [1,817] | biology, ngs, sequencing |
segment-liftover | segment-liftover | 20211021 | [1,818] | biology, genomics |
seismometer | seismometer | 0.2.1 | [1,819] | AI, utility |
SemiBin | semibin | 2.1.0 | [1,820] | bioinformatics |
SEPP | sepp | 20160614 | [1,821] | biology, phylogenetics |
Seq-Gen | seq-gen | 1.3.3 | [1,822] | biology, phylogenetics |
seq_crumbs | seq_crumbs | 20150120 | [1,823] | biology, sequencing, genomics, utility |
SeqKit | seqkit | 0.8.0, 2.0.0, 2.4.0 | [1,824] | biology, phylogenetics |
seqmagick | seqmagick | 0.8.4 | [1,825] | biology |
SeqMap | seqmap | 1.0.13 | [1,826] | biology, sequencing, ngs |
seqmule | seqmule | 1.2.6 | [1,827] | biology, sequencing |
SEQPower | seqpower | 1.1.1 | [1,828] | genomics, phylogenetics |
SeqPrep | seqprep | 0.5, 1.1 | [1,829] | biology, ngs, sequencing |
seqscreen | seqscreen | 3.3 | [1,830] | sequencing, biology |
seqtk | seqtk | 1.3, 20140729 | [1,831] | biology, genomics, ngs |
SEQuel | sequel | 1.0.1 | [1,832] | biology, ngs |
SequelQC | sequelqc | 1.1.0 | [1,833] | phylogenetics |
seqwish | seqwish | 0.7, 20190509 | [1,834] | phylogenetics |
SeqyClean | seqyclean | 1.8.10 | [1,835] | biology, ngs, sequencing |
SeSiMCMC | sesimcmc | 4.36 | [1,836] | biology, sequencing |
SExtractor | sextractor | 2.19.5 | [1,837] | astronomy |
SHAPE-MaP | shapemap | 1.2 | [1,838] | biology, phylogenetics |
SHAPEIT | shapeit | 2.12, 2.5 | [1,839] | biology, variant_calling |
SHAPEIT4 | shapeit4 | 4.2.2 | [1,840] | biology, sequencing |
ShapeMapper | shapemapper | 2.1.3, 2.1.5, 2.2.2 | [1,841] | biology, phylogenetics |
SHARCGS | sharcgs | 1.2.11 | [1,842] | biology, ngs, de_novo |
Shasta | shasta | 0.1.0 | [1,843] | phylogenetics |
SHEsisPlus | shesisplus | 1.0, 1.01 | [1,844] | biology, genomics |
shogun | shogun | 6.1.3 | [1,845] | phylogenetics |
Shortbred | shortbred | 0.9.4 | [1,846] | phylogenetics |
shortstack | shortstack | 4.0.3 | [1,847] | biology |
shovill | shovill | 1.1.0 | [1,848] | genomics, sequencing, biology |
SHRiMP | shrimp | 2.2.3 | [1,849] | biology, genomics, ngs |
shustring | shustring | 2.6 | [1,850] | biology, sequencing |
SibeliaZ | sibeliaz | 1.2.2, 1.2.3, 1.2.4 | [1,851] | biology, genomics, alignment |
SICER | sicer | 1.1 | [1,852] | biology, chip-seq |
Sickle | sickle | 1.200, 1.33 | [1,853] | biology, ngs |
Siesta | siesta | 3.2, 4.1b2, 4.1b3 | [1,854] | chemistry |
SIFT | sift | 4.0.3b | [1,855] | biology, genomics |
SIGffRid | sigffrid | 1.1 | [1,856] | phylogenetics |
SignalP | signalp | 4.1c, 5.0b, 6.0h | [1,857] | biology, phylogenetics |
SiLiX | silix | 1.2.11, 1.3.0 | [1,858] | phylogenetics |
silo | silo | 4.7 | [1,859] | library |
sim4 | sim4 | 20121010 | [1,860] | biology, genomics |
Sim4Life | sim4life | 7.0.1, 7.2.3 | [1,861] | biology, simulation |
Simka | simka | 1.5.3 | [1,862] | phylogenetics |
SimNIBS | simnibs | 3.2.1, 4.0.0, 4.1.0 | [1,863] | phylogenetics |
SimSeq | simseq | 4.12.2011 | [1,864] | biology, ngs, phylogenetics |
Simulia | simulia | 2019 | [1,865] | simulation, visualization |
SInC | sinc | 20140120 | [1,866] | biology, phylogenetics |
sine_scan | sine_scan | 1.1.1 | [1,867] | phylogenetics |
Singularity | singularity | 3.10.4 | [1,868] | workflow_automation |
SIPeS | sipes | 2.0 | [1,869] | biology, chip-seq |
SIRIL | siril | 1.2.0 | [1,870] | image processing |
sisl | sisl | 0.8.3 | [1,871] | physics, structure |
Ska2 | ska2 | 0.3.0 | [1,872] | alignment, biology, genomics |
skmer | skmer | 3.2.1 | [1,873] | genomics, biology |
Slamdunk | slamdunk | 0.4.1, 0.4.2 | [1,874] | phylogenetics |
SLAW | slaw | 20211217 | [1,875] | chemistry, spectroscopy |
Sleap | sleap | 1.3.3 | [1,876] | machine learning |
Slicer | slicer | 4.3.1, 5.0.3, 5.2.1 | [1,877] | biology, neuroscience, imaging |
slicer | slicer | 5.6.2 | [1,878] | biology, neuroscience, medicine, imaging |
slivar | slivar | 0.3.0 | [1,879] | biology |
slow5tools | slow5tools | 0.5.1, 1.1.0 | [1,880] | biology, sequencing |
SLR | slr | 1.0.0 | [1,881] | genomics |
slurm-drmaa | slurm-drmaa | 1.1.3, 1.1.4, 1.1.4.1 | [1,882] | library, scheduler, programming |
smalt | smalt | 0.7.6 | [1,883] | biology, phylogenetics |
SMARTdenovo | smartdenovo | 20180219 | [1,884] | biology, phylogenetics |
smartie-sv | smartie-sv | 20180308 | [1,885] | phylogenetics |
SMC++ | smcpp | 1.15.4 | [1,886] | biology, genomics, sequencing |
Smetana | smetana | 1.1.0 | [1,887] | phylogenetics |
SMR | smr | 1.03 | [1,888] | biology, genomics |
SMRT-SV | smrtsv2 | 2.0.0 | [1,889] | biology, ngs |
SMS | sms | 1.7 | [1,890] | biology |
Smudgeplot | smudgeplot | 0.2.4 | [1,891] | phylogenetics |
Snakemake | snakemake | 7.5.0, 8.10.8, 8.4.0 | [1,892] | biology, workflow_automation |
SNAP | snap | 2.0.0, 2.0.3, 20100728 | [1,893] | biology, variant_calling |
SNAPE-pooled | snape-pooled | 20130407 | [1,894] | biology, variant_calling |
SNeP | snep | 1.1 | [1,895] | biology, phylogenetics |
Sniffles | sniffles | 1.0.11, 1.0.6, 1.0.8 | [1,896] | phylogenetics |
Sniffles2 | sniffles2 | 2.0.6 | [1,897] | biology |
Snippy | snippy | 20160419, 4.6.0 | [1,898] | biology, phylogenetics |
SNP-Pipeline | snp-pipeline | 1.0.1 | [1,899] | biology, phylogenetics |
SNP-sites | snp-sites | 2.0.3 | [1,900] | biology, variant_calling |
snp2hla | snp2hla | 1.0.3 | [1,901] | biology, genomics |
SnpEff | snpeff | 5.0, 5.1d, 5.2e | [1,902] | biology, annotation |
snpflip | snpflip | 20190515 | [1,903] | biology, phylogenetics |
SNPGenie | snpgenie | 20190620 | [1,904] | phylogenetics |
SNPhylo | snphylo | 20140701, 3.0 | [1,905] | biology, phylogenetics |
SNPsplit | snpsplit | 0.5.0 | [1,906] | biology, sequencing |
SNPTEST | snptest | 2.5.2 | [1,907] | phylogenetics |
SOAPaligner | soapaligner | 2.21 | [1,908] | phylogenetics |
SOAPdenovo | soapdenovo | 1.05, 2.04 | [1,909] | biology, ngs |
SOAPdenovo-Trans | soapdenovo-trans | 1.01, 1.03 | [1,910] | biology, ngs |
SOAPec | soapec | 2.03 | [1,911] | biology, phylogenetics |
SOAPnuke | soapnuke | 2.1.0 | [1,912] | phylogenetics |
SOAPsplice | soapsplice | 1.10 | [1,913] | biology, ngs |
SODA | soda | 20200930 | [1,914] | biology |
SOLAR | solar | 8.4.2 | [1,915] | phylogenetics |
SomaticSeq | somaticseq | 3.6.2 | [1,916] | phylogenetics |
SortaDate | sortadate | 20190705 | [1,917] | phylogenetics |
SortMeRNA | sortmerna | 2.1, 4.0, 4.3.6 | [1,918] | biology, sequencing, ngs |
SourceTracker2 | sourcetracker2 | 2.0.1 | [1,919] | phylogenetics |
Sourmash | sourmash | 2.0.1, 4.5.0 | [1,920] | phylogenetics |
SoX | sox | 14.4.2 | [1,921] | phylogenetics |
spacemake | spacemake | 0.5.5 | [1,922] | sequencing |
SpaceRanger | spaceranger | 2.1.0, 3.0.1, 3.1.1 | [1,923] | phylogenetics |
SPAdes | spades | 3.7.1, 3.8.0, 4.0.0 | [1,924] | biology, ngs |
SparCC | sparcc | 201608 | [1,925] | biology |
Spark | spark | 2.2.0, 3.1.1 | [1,926] | utility |
sparsehash | sparsehash | 2.0.3 | [1,927] | web, programming |
SPARTA+ | sparta+ | 2.60 | [1,928] | chemistry |
Spec2nii | spec2nii | 0.3.4 | [1,929] | phylogenetics |
SpeedSeq | speedseq | 0.1.2 | [1,930] | phylogenetics |
Spidey | spidey | 20150922 | [1,931] | biology, genomics |
SpinalCordToolbox | spinalcordtoolbox | 5.4 | [1,932] | phylogenetics |
SplAdder | spladder | 2.4.2 | [1,933] | phylogenetics |
SpliceGrapher | splicegrapher | 0.2.5 | [1,934] | biology, sequencing |
SpliceTrap | splicetrap | 0.90.5 | [1,935] | biology, genomics, ngs |
SPM | spm | 12b, 8, 8r5236 | [1,936] | biology |
spruceup | spruceup | 2019.2.3 | [1,937] | phylogenetics |
Sputnik | sputnik | 1.0 | [1,938] | biology |
spyder | spyder | 4.1.4, 5.1.1, 5.3.2 | [1,939] | programming |
SQANTI | sqanti | 1.2 | [1,940] | phylogenetics |
SQANTI2 | sqanti2 | 5.0 | [1,941] | phylogenetics |
SQANTI3 | sqanti3 | 1.6, 4.2, 5.1.1 | [1,942] | phylogenetics |
SQL Developer | sqldeveloper | 4.1.2 | [1,943] | programming, database |
SQLite | sqlite3 | 3.33.0, 3.45.3, 3.8.8.2 | [1,944] | database |
squashfuse | squashfuse | 0.5.2 | [1,945] | containers, library |
SqueezeMeta | squeezemeta | 1.4.0, 1.5.2, 1.6.0 | [1,946] | phylogenetics |
squigglekit | squigglekit | 1.0.0 | [1,947] | visualization, biology |
squigglenet | squigglenet | 1.0 | [1,948] | sequencing, biology |
SRA | sra | 3.0.2, 3.0.5, 3.0.8 | [1,949] | biology, ngs |
sra-human-scrubber | sra_human_scrubber | 1.1 | [1,950] | genomics |
SRAssembler | srassembler | 1.0.0 | [1,951] | phylogenetics |
srst2 | srst2 | 0.2.0 | [1,952] | sequencing, genomics, biology |
SSM | ssm | 20210511 | [1,953] | phylogenetics |
SSPACE | sspace | 2.0, 3.0 | [1,954] | biology, ngs |
ssr_pipeline | ssr_pipeline | 0.951 | [1,955] | biology, sequencing |
SSU-ALIGN | ssu-align | 0.1.1 | [1,956] | phylogenetics |
stable-diffusion | stable-diffusion | 20221116 | [1,957] | machine_learning |
Stacks | stacks | 2.53, 2.55, 20190403 | [1,958] | biology, genomics, ngs |
stacks | stacks | 2.61, 2.64 | [1,959] | biology, genomics, ngs |
Staden | staden | 1.14.6 | [1,960] | biology, phylogenetics |
Stampy | stampy | 1.0.31 | [1,961] | biology, sequencing |
staphb-toolkit | staphb-toolkit | 1.2.0, 1.3.10, 2.0.1 | [1,962] | biology |
STAR | star | 2.7.5c, 2.7.6a, 2.7.9a | [1,963] | biology, ngs, rna-seq |
STAR-CCM+ | starccm+ | 14.04.011, 15.02.009, 8.06 | [1,964] | fluid_dynamics |
STAR-Fusion | star-fusion | 1.13.0, 1.3.1, 1.9.1 | [1,965] | biology, sequencing |
starseqr | starseqr | 0.6.7 | [1,966] | phylogenetics |
Stata | stata | 10.1, 13, 18 | [1,967] | statistics |
Strainline | strainline | 1.0 | [1,968] | biology |
Strelka | strelka | 2.9.2 | [1,969] | biology, genomics |
stringMLST | stringmlst | 0.4 | [1,970] | biology, chip-seq |
Stringtie | stringtie | 2.0.4, 2.1.3b, 2.2.3 | [1,971] | biology, ngs, sequencing, alignment |
Structure | structure | 2.3.3, 2.3.4 | [1,972] | biology, genomics |
Structure_threader | structure_threader | 1.3.10 | [1,973] | utility, structure |
stumpy | stumpy | 1.11.1 | [1,974] | library, math |
stylegan3 | stylegan3 | 20211028 | [1,975] | ai, image_processing |
SU2 | su2 | 7.0.6 | [1,976] | phylogenetics |
subphaser | subphaser | 1.2.6 | [1,977] | sequencing, biology |
Subread | subread | 2.0.0, 2.0.3, 2.0.6 | [1,978] | biology, sequencing, variant_calling |
Subversion | subversion | 1.14.2, 1.9.7 | [1,979] | revision_control |
SUMO | sumo | 1.2.0, 1.20.0, 1.9.2 | [1,980] | simulation, mapping |
SUNDIALS | sundials | 2.5.0, 3.0.0, 6.1.1 | [1,981] | math |
supercell | supercell | 20170602 | [1,982] | biology, ngs |
SuperCRUNCH | supercrunch | 1.2.1 | [1,983] | phylogenetics |
SUperLU-DIST | superlu_dist | 6.0.1, 8.2.1, 9.1.0 | [1,984] | linear algebra |
Supernova | supernova | 1.2.1, 2.0.0, 2.1.1 | [1,985] | biology, phylogenetics, ngs |
SUPPA | suppa | 2.3 | [1,986] | phylogenetics |
support | support | 24.03.20 | [1,987] | ufrc, admin, tools |
SurrealDB | surrealdb | 1.3.1, 1.5.0, 2.0.1 | [1,988] | database |
Survival_Kit | survival_kit | 6.12 | [1,989] | healthcare |
SURVIVOR | survivor | 1.0.6 | [1,990] | phylogenetics |
SVDetect | svdetect | 0.8b | [1,991] | biology, ngs, genomics |
svim | svim | 1.4.2 | [1,992] | biology |
svim-asm | svim-asm | 1.0.2 | [1,993] | biology |
svtyper | svtyper | 0.7.1 | [1,994] | biology, genomics, sequencing |
swarm | swarm | 1.2.11 | [1,995] | data_science |
Sweed | sweed | 3.3.2 | [1,996] | biology, phylogenetics |
SWIG | swig | 3.0.8, 4.1.1, 4.2.1 | [1,997] | library, programming, compiler |
SWSC-EN | swsc-en | 1.0.0 | [1,998] | phylogenetics |
Synima | synima | 20210908 | [1,999] | phylogenetics |
syri | syri | 1.5.4 | [2,000] | genomics, biology |
TACO | taco | 0.7.3 | [2,001] | phylogenetics |
Taiyaki | taiyaki | 5.0.1 | [2,002] | phylogenetics |
talesf | talesf | 20160814 | [2,003] | phylogenetics |
talon | talon | 5.0 | [2,004] | biology, sequencing |
Tandem-Genotypes | tandem-genotypes | 1.4.0 | [2,005] | phylogenetics |
Tantan | tantan | 13 | [2,006] | imaging, ngs, genomics |
Tapestri | tapestri | 2.0.1 | [2,007] | phylogenetics |
tapir | tapir | 20160825 | [2,008] | biology, phylogenetics |
TAPIS | tapis | 1.2.1 | [2,009] | biology, sequencing |
TASSEL | tassel | 5.2.20, 5.2.29, 5.2.82 | [2,010] | biology, genomics, sequencing |
TAU | tau | 2.23, 2.26, 2.26.3 | [2,011] | library, performance_analysis |
Tax4Fun | tax4fun | 0.3.1 | [2,012] | phylogenetics |
taxMaps | taxmaps | 0.1 | [2,013] | biology, phylogenetics, genomics |
TaxonKit | taxonkit | 0.13.0, 0.9.0 | [2,014] | phylogenetics |
Taxtastic | taxtastic | 0.5.7, 0.9.1 | [2,015] | biology, genomics |
tbb | onetbb | 2017_20161128, 2022.0.0 | [2,016] | library |
tbprofiler | tbprofiler | 4.4.1 | [2,017] | genomics, biology |
tcllib | tcllib | 1.18 | [2,018] | library |
tcoffee | tcoffee | 10.00.r1613, 9.03.r1318 | [2,019] | biology |
TDNAscan | tdnascan | 20210304 | [2,020] | phylogenetics |
Tecplot 360 EX | tecplot | 2015R1 | [2,021] | math, animation, fluid_dynamics, simulation |
tellseq | tellseq | 1.0.0 | [2,022] | sequencing, phylogenetics |
TEMP | temp | 20170731 | [2,023] | phylogenetics |
TEMP2 | temp2 | 0.1.4 | [2,024] | phylogenetics |
TensorFlow | ngc-tensorflow | 2.6.0, 2.7.0, 2.8.0 | [2,025] | library, math |
TESS | tess | 2.3.1 | [2,026] | biology, genomics, math |
tesseract | tesseract | 5.3.4 | [2,027] | OCR |
Test | test | 1.0 | [2,028] | shell |
TetGen | tetgen | 1.5.0 | [2,029] | modeling |
TEToolkit | tetoolkit | 1.5.1 | [2,030] | biology, sequencing |
TEtools | tetools | 20180213 | [2,031] | biology, phylogenetics |
Texlive | texlive | 20191127, 2020, 2023 | [2,032] | documentation |
textract | textract | 1.6.1 | [2,033] | data_science, file_management |
TGICL | tgicl | 2.1 | [2,034] | biology, ngs, sequencing |
TGSGapCloser | tgsgapcloser | 1.0.3 | [2,035] | phylogenetics |
the_silver_searcher | the_silver_searcher | 2.2.0 | [2,036] | search |
Themisto | themisto | 0.2.0, 1.1.0 | [2,037] | genomics, alignment |
Tiara | tiara | 1.0.2 | [2,038] | phylogenetics |
tidk | tidk | 0.2.41 | [2,039] | bioinformatics |
tiff | tiff | 3.8.0, 4.0.10, 4.6.0 | [2,040] | imaging |
tighe-r | tighe-r | 4.2, studio | [2,041] | statistics |
Tigmint | tigmint | 1.1.2 | [2,042] | phylogenetics |
TMHMM | tmhmm | 2.0 | [2,043] | biology |
Tmux | tmux | 2.9, 3.1, 3.4 | [2,044] | programming |
TNTBLAST | tntblast | 2.04 | [2,045] | biology |
ToFU2 | tofu2 | v17 | [2,046] | biology, ngs, sequencing |
toil | toil | 3.3.0, 3.3.3 | [2,047] | biology |
Tombo | tombo | 1.4, 1.5, 1.5.1 | [2,048] | biology, genomics, ngs |
topd | topd | 4.6 | [2,049] | phylogenetics |
Tophat | tophat | 2.1.0, 2.1.1, 2.1.2 | [2,050] | biology, ngs, sequencing |
torch-geometric | torch-geometric | 1.3.2, 2.0.4 | [2,051] | math, machine_learning |
TotalView | totalview | 8.12 | [2,052] | programming |
TPMcalculator | tpmcalculator | 0.0.3 | [2,053] | phylogenetics |
TPP | tpp | 4.7.0, 4.7.1, 5.0.0 | [2,054] | biology, chemistry, spectroscopy |
TraCeR | tracer | 20160519 | [2,055] | biology, phylogenetics |
TrackTools | tracktools | 2011 | [2,056] | utility |
TrackVis/DTK | trackvis | 0.5.2.2, 0.6.0.1 | [2,057] | biology, neuroscience, imaging |
Tracula | tracula | 5.3.2014_05_26 | [2,058] | biology, neuroscience, imaging |
traitRate | traitrate | 1.1 | [2,059] | biology, genomics |
Trans-ABySS | transabyss | 2.0.1 | [2,060] | biology, phylogenetics |
TransDecoder | transdecoder | 5.3.0, 5.4.0, 5.5.0 | [2,061] | biology, ngs |
TRANSIT | transit | 2.5.2, 3.2.3 | [2,062] | phylogenetics |
Transrate | transrate | 1.0.1, 1.0.3 | [2,063] | biology, assembly |
TransVar | transvar | 2.3.3 | [2,064] | biology, phylogenetics |
TreeBreaker | treebreaker | 20160621 | [2,065] | biology, phylogenetics |
TreeMix | treemix | 1.12 | [2,066] | biology, phylogenetics |
treePL | treepl | 20150305 | [2,067] | biology, phylogenetics |
TREEPUZZLE | treepuzzle | 5.3 | [2,068] | biology, phylogenetics |
TreeShrink | treeshrink | 1.3.1, 1.3.2, 1.3.9 | [2,069] | phylogenetics |
TreeTime | treetime | 0.10.1, 0.7.5, 0.8.1 | [2,070] | phylogenetics |
trelis | trelis | 16.3 | [2,071] | math |
TRF | trf | 4.04, 4.09.1 | [2,072] | biology, genomics |
trgt | trgt | 0.4.0 | [2,073] | genetics, biology |
Trilinos | trilinos | 12.6.4, 14.4.0, 16.6.0 | [2,074] | math |
Trim Galore | trim_galore | 0.5.0, 0.6.10, 0.6.5 | [2,075] | biology, ngs |
trim_isoseq_polya | trim_isoseq_polya | 0.0.3 | [2,076] | biology, genomics, sequencing |
trimAl | trimal | 1.2, 1.4.1 | [2,077] | biology, genomics, alignment |
trimesh | trimesh | 3.20.2 | [2,078] | graphics, math |
TriMetAss | trimetass | 1.1 | [2,079] | biology, ngs |
Trimmomatic | trimmomatic | 0.33, 0.36, 0.39 | [2,080] | biology, ngs |
Trinity | trinity | r20130225, r20131110, r20140413 | [2,081] | biology, ngs, sequencing, rna-seq |
Trinotate | trinotate | 3.0.1, 3.2.0, 4.0.0 | [2,082] | biology |
triobinning | triobinning | 0.2.3 | [2,083] | genomics, biology |
TRIPLEC | triplec | 1.0 | [2,084] | biology |
TRITONSERVER | tritonserver | 21.08, 23.01 | [2,085] | machine_learning |
tRNAscan-Se | trnascan-se | 1.23, 2.0.12 | [2,086] | biology, genomics, annotation |
TRUST4 | trust4 | 1.0.2b | [2,087] | phylogenetics |
trvz | trvz | 0.4.0 | [2,088] | genetics, biology |
Trycycler | trycycler | 0.4.2 | [2,089] | phylogenetics |
TURBOMOLE | turbomole | 7.4.1 | [2,090] | chemistry |
TWINSCAN | twinscan | 4.1.2 | [2,091] | biology, genomics |
Ubuntu | ubuntu | 20.04, 22.04, 24.04 | [2,092] | linux |
UCSC | ucsc | 20200320, 20210803 | [2,093] | genomics |
ucsc-fafiltern | ucsc-fafiltern | 377 | [2,094] | phylogenetics |
ucsc-maskoutfa | ucsc-maskoutfa | 377 | [2,095] | phylogenetics |
UCX | ucx | 1.11.2, 1.15.0, 1.9.0 | [2,096] | programming, library |
UDUNITS | udunits | 2.2.17 | [2,097] | library, data_science, math |
UFCG | ufcg | 1.0.3, 1.0.5 | [2,098] | biology, genomics |
ufraw | ufraw | 0.22 | [2,099] | data_mining |
ugtm | ugtm | 1.1.6 | [2,100] | statistics, modeling |
UKFractography | ukfractography | 20200127 | [2,101] | phylogenetics |
umi-tools | umi-tools | 0.5.5, 1.1.4, 1.1.5 | [2,102] | phylogenetics |
UMICollapse | umicollapse | 02072021 | [2,103] | chemestry |
UNAFold | unafold | 3.8 | [2,104] | biology, genomics, rna |
Unanimity | unanimity | 20171108, 3.4.1 | [2,105] | programming, library, compiler |
UNCALLED | uncalled | 2.2 | [2,106] | biology, genomics |
Unicycler | unicycler | 0.4.8 | [2,107] | phylogenetics |
Unrar | rar | 0.0.1, 4.20 | [2,108] | utility |
unrealengine editor | unrealengine | 5.2.1 | [2,109] | programming, design, digitaltwin |
uproc | uproc | 1.2.0 | [2,110] | biology, genomics |
UPSCAYL | upscayl | 2.5.5, 2.8.1, 2.9.1 | [2,111] | image processing |
uropa | uropa | 4.0.2 | [2,112] | genomics, sequencing, biology |
USEARCH | usearch | 9.0.2132, 9.1.13, 9.2.64 | [2,113] | biology, alignment, sequencing |
UShER | usher | 0.1.4, 0.4.1, 0.5.2 | [2,114] | phylogenetics |
V-Phaser | vphaser2 | 02112013 | [2,115] | biology, phylogenetics |
v-pipe | v-pipe | 2.0.0, 2.99.3 | [2,116] | biology, genomics, sequencing |
Valgrind | valgrind | 3.11.0, 3.15.0, 3.8.1 | [2,117] | programming |
Valouev | valouev | 20160325 | [2,118] | biology, phylogenetics |
vamb | vamb | 3.0.2 | [2,119] | biology |
VAMPIR | vampir | 9.1 | [2,120] | performance_analysis |
VarDictJava | vardictjava | 1.6.0, 20160521, 20170531 | [2,121] | biology, phylogenetics |
VARI | vari | 0.7.0 | [2,122] | math, visualization |
varnorm | varnorm | 0.21 | [2,123] | biology |
varpipe-wgs | varpipe-wgs | 20230222 | [2,124] | sequencing, biology |
VarScan | varscan | 2.3.6 | [2,125] | biology, ngs |
VarSim | varsim | 0.8.4, 0.8.6 | [2,126] | phylogenetics |
VarSimLab | varsimlab | 20180220, 20180921 | [2,127] | biology, simulation, genomics |
vasp | vasp | 5.4.4, 6.1.0, 6.2.0 | [2,128] | chemistry |
VASP | vasp_el8 | 5.4.4, 6.4.1, 6.4.3 | [2,129] | chemistry |
vaspkit | vaspkit | 1.2.5, 1.4.1 | [2,130] | phylogenetics |
VAST-TOOLS | vast-tools | 2.5.1, 20150506 | [2,131] | biology, rna-seq, ngs |
VCF-kit | vcf-kit | 0.2.6 | [2,132] | phylogenetics |
vcf-validator | vcfvalidator | 0.6 | [2,133] | biology, phylogenetics |
vcfanno | vcfanno | 0.2.8, 0.3.3 | [2,134] | biology, phylogenetics |
vcflib | vcflib | 1.0.1 | [2,135] | biology, genomics |
vcftools | vcftools | 0.1.15, 0.1.16, 0.1.9 | [2,136] | biology, genomics |
vcontact | vcontact | 20190512 | [2,137] | phylogenetics |
VDJtools | vdjtools | 1.1.7, 1.2.1 | [2,138] | biology, phylogenetics |
Velocyto | velocyto | 0.17 | [2,139] | biology, RNA seq |
Velvet | velvet | 1.2.10, 1.2.10-long | [2,140] | biology, genomics |
VEP | vep | 83, 88.8, 92 | [2,141] | biology, genomics, ngs |
Verkko | verkko | 1.3.1 | [2,142] | genomics |
vermouth-martinize | vermouth-martinize | 0.11.0 | [2,143] | biology, molecular |
Vermouth-martinize | vermouth-martinize | 0.7.2 | [2,144] | phylogenetics |
VeryFastTree | veryfasttree | 3.0.1 | [2,145] | phylogenetics |
VFUparr | vfuparr | 20240320 | [2,146] | sequencing, biology |
vg | vg | 1.45.0, 1.49.0, 1.55.0 | [2,147] | phylogenetics |
vibrant | vibrant | 1.2.0 | [2,148] | genomics |
ViennaRNA | viennarna | 2.2.6, 2.4.18 | [2,149] | biology, rna-seq |
ViewBS | viewbs | 0.1.10, 0.1.9 | [2,150] | phylogenetics |
vigor4 | vigor4 | 20200702 | [2,151] | biology, annotation |
Vim | vim | 8.1.1566, 8.2.2465, 9.0.1946i | [2,152] | programming, language |
vina-gpu | vina-gpu | 20230530 | [2,153] | biology |
viralmsa | viralmsa | 1.1.10, 1.1.12, 1.1.14 | [2,154] | phylogenetics |
VIRCLUST | virclust | 2.0 | [2,155] | biology, annotation |
viromescan | viromescan | 2015 | [2,156] | genomics, biology |
VirSieve | virsieve | 20210406 | [2,157] | biology, pipeline |
virsorter | virsorter | 2.2.3 | [2,158] | genomics |
VirtualCell | virtualcell | 7.1 | [2,159] | phylogenetics |
VIRULIGN | virulign | 1.0.2 | [2,160] | phylogenetics |
VirusDetect | virusdetect | 1.7 | [2,161] | phylogenetics |
VirusFinder | virusfinder | 2.0 | [2,162] | biology, phylogenetics |
visit | visit | 3.3.3, 3.3.3-mpi, 3.3.3_mpi | [2,163] | visualization, animation |
VISPR | vispr | 0.4.14 | [2,164] | phylogenetics |
vmamba | vmamba | 2.0 | [2,165] | machine_learning |
VMD | vmd | 1.9.1, 1.9.3, 1.9.4 | [2,166] | visualization, animation, graphics |
vray | vray | 6.10.04 | [2,167] | graphics |
vscode | vscode | 1.86.2, 1.87, 1.92 | [2,168] | programming |
VSearch | vsearch | 2.22.1, 20151022, 20161209-2.3.4 | [2,169] | biology, ngs |
vt | vt | 0.57721, 20140903, 20160129 | [2,170] | biology, genomics |
VTC | vtc | 0.9.3 | [2,171] | biology |
VTK | vtk | 9.1.0, 9.2.6, 9.3.0 | [2,172] | biology, neuroscience, imaging |
w2rap-contigger | w2rap-contigger | 20161124 | [2,173] | biology, genomics |
Wannier90 | wannier90 | 1.2, 2.1.0, 3.1.0 | [2,174] | computational Physics |
WarpedLMM | warpedlmm | 0.21 | [2,175] | modeling |
WaveGAN | wavegan | 20190829 | [2,176] | machine_learning, audio, GAN |
WDSSII | wdss2 | 5, 6 | [2,177] | climate |
WebLogo | weblogo | 3.3, 3.5.0, 3.7 | [2,178] | biology, sequencing, graphics |
webodm | webodm | 20240718 | [2,179] | graphics |
Weka | weka | 3.8, 3.8.5 | [2,180] | statistics, machine_learning |
Wengan | wengan | 0.2 | [2,181] | biology, genomics |
wfmash | wfmash | 0.13.0 | [2,182] | phylogenetics |
wgd | wgd | 1.1.1 | [2,183] | phylogenetics |
WGS Assembler | wgs | 8.3rc1.r4638, 8.3rc2 | [2,184] | biology, genomics |
Wgsim | wgsim | 0.3.1-r13 | [2,185] | biology, phylogenetics |
WHAMM | whamm | 0.14a | [2,186] | biology, phylogenetics |
WhatsHap | whatshap | 1.1, 2.1 | [2,187] | biology, phylogenetics |
whiteboxtools | whiteboxtools | 1.5.0 | [2,188] | phylogenetics |
widis-lstm-tools | widis-lstm-tools | 0.4 | [2,189] | ML |
Wine | wine | 4.0.0, 7.0.0 | [2,190] | linux, utility |
Wise | wise | 2.2.0, 2.4.1 | [2,191] | biology, genomics |
WIsH | wish | 1.0 | [2,192] | phylogenetics |
WoLFPSort | wolfpsort | 0.2 | [2,193] | phylogenetics |
WOMBAT | wombat | 20180118 | [2,194] | biology, phylogenetics |
workbench | workbench | 4.1.1 | [2,195] | modeling, simulation |
wtdbg | wtdbg | 2.1, 2.4, 2.5 | [2,196] | phylogenetics |
WU BLAST | wublast | 2.0 | [2,197] | biology |
Wub | wub | 0.2.0, 0.4.0 | [2,198] | biology, genomics, ngs |
xander | xander | 20151222 | [2,199] | biology, phylogenetics |
Xapian | xapian | 1.4.4 | [2,200] | library |
XCrySDen | xcrysden | 1.5.60 | [2,201] | material_science |
Xerces | xerces | 3.1.4 | [2,202] | phylogenetics |
xesmf | xesmf | 0.6.2 | [2,203] | math, climate |
xlsx2csv | xlsx2csv | 0.8.0 | [2,204] | utility |
xpclr | xpclr | 1.0, 1.1.1 | [2,205] | phylogenetics |
xppaut | xppaut | 8.0 | [2,206] | math |
xroms | xroms | v0.5.4 | [2,207] | geospatial |
xtea | xtea | 0.1.9 | [2,208] | genomics |
Xterm | xterm | 1.1 | [2,209] | utility |
xwalk | xwalk | 0.6 | [2,210] | biology |
XWAS | xwas | 3.0 | [2,211] | phylogenetics |
XY-Meta | xy-meta | 20200413 | [2,212] | phylogenetics |
XZ | xz | 5.2.2 | [2,213] | compression, library |
yagcloser | yagcloser | 1.0.0 | [2,214] | biology, genomics, assembly |
YAGO | yago | 4 | [2,215] | data_science |
YAHA | yaha | 0.1.82 | [2,216] | biology, ngs |
Yaha | yahs | 1.1 | [2,217] | biology |
YAK | yak | 0.1 | [2,218] | phylogenetics |
YASM | yasm | 1.3.0 | [2,219] | programming |
YASRA | yasra | 2.33 | [2,220] | biology, ngs, sequencing |
ydata-profiling | ydata-profiling | 4.6.1 | [2,221] | biology, ai, machine learning |
yolo | yolo | 10.0, 8.2 | [2,222] | machine_learning |
yolo-nas | yolo | NAS | [2,223] | machine_learning |
yolov4_darknet | yolov4_darknet | 4-pre | [2,224] | machine_learning |
yolov5 | yolo | 7.0, 8, 8.1 | [2,225] | machine_learning |
Z1Plus | z1plus | 1.0 | [2,226] | molecular_dynamics |
Zagros | zagros | 1.0.0 | [2,227] | biology, phylogenetics |
Zbar | zbar | 0.23.90 | [2,228] | ai, image_processing, imaging |
ZEO++ | zeo++ | 0.2.2 | [2,229] | chemistry |
ZeroSum | zerosum | 20231113 | [2,230] | programming |
zorro | zorro | 2.2 | [2,231] | biology, sequencing |
Zstd | zstd | 1.5.0 | [2,232] | phylogenetics |
ZUMIS | zumis | 2.6.0 | [2,233] | biology, ngs, sequencing |