Installed Software

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Installed Software List

Last updated 2014-08-08.

Note: Click on the icons to the right of the column headings to sort the table.

Name Version [1] Website Category
AbInit 6.12.3 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.4, 1.3.7 [2] Biology, NGS
ALLPATHS-LG 42316, 44837 [3] Biology, NGS
AFNI 2011_12_21_1014 [4] Biology, Statistics, Imaging, Neurology
Amber 11, 12, 14 [5] Simulation, chemistry
AMOS 3.1.0 [6] Biology, Genomics, NGS
ANNOVAR 20120621,20121023,20130321 [7] Biology, Genomics
Atlas 3.10.1, 3.11.17 [8] Library, Math
Amuse 6.0 [9] Astrophysics
Affymetrix Power Tools 1.15.0 [10] Biology, Genomics, Microarray
AtomEye 3 [11] Material Science
ATRAM 20140624 [12] Biology, NGS
Augustus 2.6 [13] Biology, NGS
BamBam 1.0 [14] Biology, NGS
Bamstats 20140602 [15] Biology, NGS
Bamtools 2.1.1 [16] Biology, NGS
BamUtil 1.0.2 [17] Biology, NGS
BayesRate 1.3.43 [18] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [19] Network file transfer
Bcftools 20140618 [20]] Biology, Genomics, NGS
BEAGLE 3.2.2 [21] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [22] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [23] Biology, NGS
BEST 2.3 [24] Biology, Phylogenetics
BETA 1.0.5 [25] Biology, NGS
BFAST 0.7.0 [26] Biology, NGS
Bismark 0.7.4, 0.7.7 [27] Biology, Methylation, NGS
Bioconductor Latest [28] Biology, R, Statistics
BioPerl 1.006901 [29] Biology, Perl
BioPython 1.59 [30] Biology, Python
BLASR 20130815 [31] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [32] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [33] Biology, Annotation
BLAT 20120524 [34] Biology, Sequence alignment
Blender 2.63 [35] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [36] C++, Library
Bowtie 0.12.8, 0.12.9, 1.0.0 [37] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3 [38] Biology, NGS
BRANCH 1.8.1 [39] Biology, NGS, Mapping
Bwa 0.6.1, 0.7.9a, 0.7.10 [40] Biology, NGS
Camino 20140723 [41] Biology, Neuroscience, Imaging
CAP3 20120705 [42] Biology, sequence assembly
CASAVA 1.8.2 [43] Biology, NGS
CD-HIT 4.6 [44] Biology, Genomics
CDO 1.6.1 [45] Climate
CEAS 1.0.2 [46] Biology, Genomics
CellProfiler 2.0 [47] Biology, Image Analysis
Charmm 36a3 [48] Simulation, Chemistry
Chartdirector 5.1.0 [49] Graphics
CIMS 4.1.2 [50] Biology, Genomics
Circos 0.63-pre11 [51] Biology, Visualization
CisGenome 2.0 [52] Biology, Genomics, Peak Calling
CLHEP 2.2.0.1 [53] High Energy Physics
ClonalFrame 1.1, 1.2 [54] Biology, Genomics, NGS
ClustalW 2.1 [55] Biology, Genomics
Clview 20130402 [56] Biology, Genomics
CMake 2.8.8 [57] Programming, Build System
CNVSeq 20110715 [58] Biology, NGS
Coevol 1.3c, 1.4b [59] Biology, Phylogenetics
CoMap 1.4.1 [60] Biology, Genomics
CONCOCT 0.3.1 [61] Biology, Genomics
Consed 23.0 [62] Biology, Genomics
covNMR 2014 [63] Biochemistry
CUDA 4.2, 5.5 [64] Programming, Graphics
Cufflinks 1.3.0, 2.0.2, 2.2.1 [65] Biology, NGS
Cutadapt 1.1 [66] Biology, NGS
DAKOTA 5.4.0 [67] Computational Science
DCMTK 3.6.0 [68] Biology, Neuroscience, Imaging
DDSCAT 7.3.0 [69] Astrophysics
Delft3D 3621 [70] Hydrodynamics, Physics
Desmond 3.0.3.1 [71] Simulation, Biology, Chemistry
Dalton 2011 [72] Quantum Chemistry
DiffReps 1.55.4 [73] Biology, NGS, ChIP-Seq
Dindel 1.01 [74] Biology, NGS
DIYABC many [75] Biology, Genomics
Dlpoly 4.03.4 [76] Simulation, Biology, Chemistry
DNA Clust 3.0 [77] Biology, Genomics
Dock 6.5, 6.6 [78] Chemistry, ligand binding prediction
DSSP 2.2.1 [79] Biology, Molecular Dynamics
DTI-TK 2.3.1 [80] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [81] Biology, NGS
EIGENSOFT 4.2, 5.0.1 [82] Biology, Population
emboss 6.5.7 [83] Biology, multi-tool suite
eQTLA 1.1 [84] Biology, Genomics
Espresso 5.0.1 [85] Modeling, Physics
ESPRIT 201211 [86] Biology, NGS, Metagenomics
ETE2 2.1 [87] Biology, Phylogenetics
Eval 2.2.8 [88] Biology, Genomics, GUI
ExaML 1.0.3, 1.0.5, 1.0.12 [89] Biology, Phylogenetics
Exonerate 2.2.0 [90] Biology, Genomics
FAR 2.15 [91] Biology, Genomics
FASTA 34.26.5, 36.3.6d [92] Biology, Genomics
FastML 3.0 [93] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [94] Biology, NGS
FastTree 2.1.7 [95] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [96] Biology, NGS
fcGENE 1.0.7 [97] Biology, Genomics, SNP
Ferret 6.82 [98] Oceanography, Meteorology
FFmpeg 2.1.3 [99] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [100] Math, Library, C++
FLASH 1.2.10 [101] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [102] Simulation, Fluid Dynamics
FragGeneScan 1.16 [103] Biology, NGS, Genomics
FreeBayes 0.9.6 [104] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [105] Biology, Neurology, Imaging
FSL 5.0.2.2 [106] Biology, Neurology, Imaging
Garli 2.0, 2.01 [107] Biology, Phylogenetics
GASVPro 201310 [108] Biology, NGS, Genomics
GATE 7.0 [109] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1 [110] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [111] Modeling, Computational Chemistry
Geant4 4.10 [112] Physics
GEM 20130406 [113] Biology, NGS
GEMINI 4.6.6a [114] Biology, Genomics, Genetics
GenBank Tools 20140130 [115] BIology< Genomics
GeneMark 2012.04 [116] Biology, Genomics, Metagenomics
Genewise 2.2.0 [117] Biology, Genomics, Annotation
GenomicTools 2.7.0 [118] Biology, NGS
Git 1.8.2.1 [119] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [120] Biology, Genomics
GnuPlot 4.6.0 [121] Graphics, Plotting, Programming
Grace 5.1.22 [122] Graphics, plotting, 2D
GrADS 2.0.1 [123] Earth Science
GraphViz 2.38.0 [124] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [125] Chemistry, Modeling, Simulation
GSL 1.15 [126] Library, Math, C++, C
GULP 4.0 [127] Material Science
HaMStR v8b [128] Biology, Genomics
Hapsembler 2.21 [129] Biology, Genomics, NGS
HDF5 1.8.9, 1.8.12 [130] Library, Data
HMMER3 3.0 [131] Biology, Genomics
HMMSplicer 0.9.5 [132] Biology, Genomics
HOMER 4.2 [133] Biology, Genomics
HTSeq 0.5.3p3, 0.6.1p1 [134] Biology, NGS
HyPhy 2.1.2.28 [135] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [136] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [137] Biology, NGS
IM and IMa 20091217 [138] Biology, Population
IMa2 20120827 [139] Biology, Population
ImageMagick 6.8.8-9 [140] Image manipulation
Intel Compilers 11.1, 2012 [141] Programming, Compilers
IOAPI 3.1 [142] Meteorology
Iprscan 4.8 [143] Biology, Genomics
ITK 4.3.1 [144] Biology, Genomics
ITK-SNAP 3.0.0 [145] Biology, Neuroscience, Imaging
JAGS 3.3.0 [146] Statistics
Java 1.6.0_31, 1.7.0_02 [147] Java Development Kit
Kent 20120524 [148] Biology, NGS
Kmer 1934 [149] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [150] Molecular Dynamics Simulation
Last 193, 247 [151] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [152] Biology, NGS
LIBSVM 3.12 [153] Machine Learning
LSC 0.3, 0.3.1 [154] Biology, NGS, Error correction
Loci 3.3 [155] Fluid Dynamics
LS-DYNA 700, 711 [156] Physics
MACH 1.0.18 [157] Biology, Genomics
MACS 1.4.2 [158] Biology, ChIP-Seq
mafft 7.037, 6.903 [159] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [160] Biology, Annotation, Genomics
Maq 0.7.1 [161] Biology, NGS
Matlab 2012a, 2013a, 2014a [162] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [163] BIology, NGS
MCarts 1.0.2 [164] Biology, Genomics, Markov models
MCNP 5, 6b2 [165] Physics
MCNPX 2.7.0, 2.7.0-i8 [166] Physics
Meme 4.8.1 [167] Biology, Motifs, Sequence analysis
Mercurial 2.7 [168] Development, Revision Control
Metabin 1.0 [169] Biology, Metagenomics
MetaCluster 5.0beta [170] Biology, Metagenomics
MetaVelvet 1.2.01 [171] Biology, NGS
MetaGeneMark 2012.04 [172] Biology, Genomics
Mfold 3.6 [173] Biology, Genomics
Midnight Commander 4.6.1 [174] Tools, Utilities
Migrate-n 3.3.0 [175] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [176] Biology, NGS
MISO 0.4.4, 0.4.9 [177] Biology, NGS
MSMBuilder 2.5.1 [178] Molecular Dynamics
Modeller 9.11, 9.13, 9.14 [179] Biology, Modeling
Molden 5.0 [180] Molecular, electronic structure
mosaik 2.1.33 [181] Biology,NGS
Mothur 1.31.2 [182] Biology, Microbial Ecology
MP-EST 1.4 [183] Biology, Phylogenetics
mpiP 3.4.1 [184] Parallel Computing
MrBayes 3.2.1 [185] Biology, Phylogenetics
MRIcron 201306 [186] Biology, MRI, Imaging
MUMmer 3.23 [187] Biology, Genomics
MUSCLE 3.8.31 [188] Biology, Genomics
NAMD 2.9 [189] Simulation, Chemistry, Biology
Nbody 6 [190] Astronomy
NCBI C++ Toolkit 12.0.0 [191] Biology, C++, Development
NCL 6.1.2 [192] Atmosphere Science
NCO 4.2.1, 4.4.3 [193] Data exchange tools
NetCDF 4.2 [194] Data exchange, Tools
Newbler 2.6, 2.7 [195] Biology, NGS
Nexus NCL 2.1.18 [196] Biology, Phylogenetics, Library
NMRPipe 7.9 [197] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [198] Biology, NGS
Oases 0.2.08 [199] Biology, NGS
Olego 1.1.2, 1.1.5 [200] Biology, NGS, RNA-Seq
Octave 3.6.4 [201] Numerical Computation
OpenBabel 2.3.2 [202] Biology, Chemistry
OpenCV 2.4.8 [203] Computervision
OpenFOAM 2.1.1 [204] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [205] Biology, Genomics
PAML 4.7 [206] Biology, Phylogenetics
ParaView 4.1.0 [207] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [208] Biology, Phylogenetics, Evolution
Parflow v615 [209] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [210] Biology, Genomics
PeakSplitter 1.0 [211] Biology, Chip-Seq
PDT 3.18 [212] Programming, Profiler
Perl 5.16.0 [213] Programming, Language
PerM 0.4.0 [214] Biology, NGS
PETSc 2.3, 3.3 [215] Math, Numerical solvers
Phenix 1.8.1069 [216] Crystallography
PHITS 2.52 [217] Physics
PhyloBayes 3.3f, 1.4f MPI [218] Biology, Phylogenetics
PhyML 3.0, 20121109 [219] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [220] Biology, NGS
Preseq 0.0.4 [221] Biology, NGS
ProBABEL 0.4.2 [222] Biology, Genomics, GWAS
Proovread 1.03rcl [223] Biology, Genomics, NGS
Proteinortho 4.26 [224] Biology, Genomics
python 2.6.8, 2.7.3 [225] Programming, scripting, language
QIIME 1.5.0 [226] Biology, Ecology
QT 4.8.3 [227] Computer Science
Quickquartet 1.0.0 [228] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [229] Statistics, Programming
R8S 1.71 [230] Biology, Evolution
RADICAL 0.2 [231] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [232] Biology, Phylogenetics
RepeatMasker 3.3.0 [233] Biology, Genomics
Reptile 1.1 [234] Biology, NGS, error correction
riboPicker 0.4.3 [235] Biology, Sequence
RNAhybrid 2.1.1 [236] Biology, Genomics
ROOT 6.0 [237] Data Analysis
RSEG 0.4.8 [238] Biology, NGS
Sailfish 0.6.3 [239] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [240] Biology, NGS
SAS 9.3 [241] Statistics, Graphing
SATe 2.2.7 [242] Biology, Phylogenetics
Sharcgs 1.2.11 [243] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [244] Simulation, chemistry
SCons 2.3.0 [245] Programming, Build System
SeqPrep 0.5 [246] Biology, NGS
SEQuel 1.0.1 [247] Biology, NGS
Seqtk 20140729 [248] Biology, NGS
SeqyClean 1.8.10 [249] Biology, NGS, quality filter
Sickle 1.200 [250] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [251] Simulation, Physics, Ab Initio
SIFT 4.0.3b [252] Biology, Genomics
Silo 4.7 [253] Library, Data
Slicer 4.3.1 [254] Biology, Imaging
SMALT 0.7.6 [255] Biology, NGS
Snap 20100728 [256] Biology, Genomics
SOAPdenovo 1.05 [257] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [258] Biology, NGS
SparCC 201402 [259] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [260] Biology, NGS
Spanki 0.4.1, 0.4.3 [261] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [262] Chemistry
SPIMAP 1.1 [263] Biology, Phylogenetics
SpliceTrap 0.90.5 [264] Biology, NGS, RNA-Seq
SPM 8 [265] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [266] Biology, Genomics
SRA 2.1.10 [267]] biology, NGS
SSPACE 2.0 [268] Biology, NGS
Stacks 0.9995 [269] Biology, Genomics, NGS
STAR 2.3.0e [270] Biology, NGS, Alignment
STAR-CCM+ 8.06 [271] Mechanical Engineering
Stata 10.1, 13 [272] Statistics, Data analysis
Stringtie 0.97 [273] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [274] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [275] Numerical Solver
swak4Foam 2.x [276] Fluid Dynamics
Swig 2.0.9 [277] Programming, C, C++, Python
Syzygy 1.2.7 [278] Biology, Genomics
TAU 2.21.4, 2.23 [279] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [280] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [281] Biology, Genomics, Markov
tgicl 2.1 [282] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [283] Biology, NGS
Totalview 8.12.0 [284] Computer Science
TPP 4.7.0 [285] Bioinformatics, MassSpec
TreeFix 1.1.7 [286] Biology, Phylogenetics
TRF 4.04 [287] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [288] Math Algorithm
Trimmomatic 0.22, 0.32 [289] Biology, NGS
Trinity r20131110, r20140413 [290] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [291] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [292] Biology, Sequence analysis
Valgrind 3.9.0 [293] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [294] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [295] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [296] Biology, NGS
vmd 1.9.1 [297] Biology, Visualization
Wannier90 1.2, 2.0.0 [298] Computational Physics
WebLogo 3.3 [299] Biology, Genomics
WDSSII 1 [300] Meteorology
WIEN2k 12.1 [301] Material Science, Chemistry
wgs 7.0.1.22 [302] Biology, NGS
wublast 2.0 [303] Biology, Sequence Alignment
Yambo 3.3.0 [304] Physics
Yasra 2.32 [305] Biology, NGS
  1. Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.