Installed Software

The following is a list of the installed software at the UF HPC Center.

Last updated 2012-06-29.

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

Software

Name	Version	Website	Category	EL5	EL6
Abaqus	6.6-1, 6.9-2	[1]	Simulation	X
Abyss	1.3.1	[2]	Biology, NGS	X
ADMB	9.1, 10.0, 10.1	[3]	Modeling, math	X
ALLPATHS-LG	39099, 40122, 41655	[4]	Biology, NGS	X
Amber	10,11.old, 11, 12	[5]	Simulation, chemistry	X
Amos	3.0.0	[6]	Biology, Genomics	X
ANNOVAR	20120308	[7]	Biology, Genomics	X
Ansys	9.0, 10.0	[8]	Simulation, Engineering	X
antlr	2.7.7, 3.1.3	[9]	Linguistics, Parser	X
arachne	37618	[10]	Biology, Genomics	X
Bamtools	2.1.0	[11]	Biology, NGS	X
BamUtil	1.0.2	[12]	Biology, NGS	X
BayesPhylogenies	2.0	[13]	Biology, Phylogenetics	X
beast	1.6.2, 1.7.0, 1.7.1	[14]	Biology, Phylogenetics	X
BEDTools	2.16.2	[15]	Biology, NGS	X
BFAST	0.7.0	[16]	Biology, NGS	X
Bioconductor	2011-11-16	[17]	Biology, R, Statistics	X
BioPerl	1.006901	[18]	Biology, Perl	X
Biopython	1.59	[19]	Biology, Python	X
bioscope	1.0.1, 1.2.1	ABI	Biology, NGS	X
Blast	2.2.24, 2.2.25, 2.2.26	[20]	Biology, Sequence alignment	X
Blast2go	2.5.0	[21]	Biology, Annotation	X
BLAT	34	[22]	Biology, Sequence alignment	X
Boost	1.38.0, 1.46.1, 1.48.0, 1.49.0	[23]	C++, Library	X
bwa	0.5.9, 0.5.10, 0.6.0 (default)	[24]	Biology, NGS	X
Bowtie	0.12.7, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5	[25]	Biology, NGS	X
BreakDancer	1.1	[26]	Biology, NGS, Genomics	X
CAP3	20071015	[27]	Biology, sequence assembly	X
CASAVA	1.8.2	[28]	Biology, NGS	X
CD-HIT	4.5.7	[29]	Biology, Genomics	X
CEGMA	2.3	[30]	Biology, Genomics, Annotation	X
CGATools	1.5.0.31	[31]	Biology, Genomics	X
Charmm	35b2	[32]	Simulation, Chemistry	X
Circuit	3.5.1, 3.5.7	[33]	GIS	X
CisGenome	2.0	[34]	Biology, Genomics, Peak Calling	X
CMake	2.8.5	[35]	Programming	X
CNV-seq	07.15.11	[36]	Biology, NGS	X
CNVnator	0.2.5	[37]	Biology, NGS	X
CPMD	3.11.1	[38]	Simulation, Chemistry	X
Cufflinks	1.0.3, 1.1.0, 1.3.0	[39]	Biology, NGS	X
Cutadapt	1.1	[40]	Biology, NGS	X
dar	2.3.9	[41]	Backup	X
deFuse	0.4.3	[42]	Biology, RNA-seq	X
Desmond	2.4.2.1	[43]	Simulation, Biology, Chemistry	X
Dindel	1.01	[44]	Biology, NGS, Genomics	X
dlpoly	3.0.9	[45]	Simulation, Biology, Chemistry	X
dock	6.3, 6.4, 6.5	[46]	Chemistry, ligand binding prediction	X
emacs	21.4.1, 23.4.1	[47]	The Emacs editor	X
EMAN2	2.04	[48]	Biology, image processing	X
emboss	6.4.0	[49]	Biology, multi-tool suite	X
espresso	3.0, 3.2.2, 4.0.4, 5.0	[50]	Modeling, Physics	X
Exonerate	2.2	[51]	Biology, Genomics	X
FAR	2.15	[52]	Biology, Genomics	X
FASTA	34.26.5	[53]	Biology, Genomics	X
fastx_toolkit	0.0.13.1	[54]	Biology, NGS	X
FastQC	0.9.6, 0.10.0	[55]	Biology, NGS	X
fftw	2.1.5, 3.1.2	[56]	Math, Library, C++	X
fluent	6.3.26	[57]	Simulation	X
FragGeneScan	1.16	[58]	Biology, NGS	X
FreeBayes	0.9.4	[59]	Biology	X
gadget	2.0.4, 2.0.5	[60]	Software Development	X
gamess	11-Aug11	[61]	Quantum Chemistry	X
garli	2.0	[62]	Biology, Phylogenetics	X
GATK	1.4.30	[63]	Biology, NGS	X
gulp	4.0.3	[64]	Modeling/simulation, Chemistry	X
gaussian	E01, G03, G09-A.02, G09-C.01	[65]	Modeling, Computational Chemistry	X
Geneid	1.4	[66]	Biology, Genomics, Annotation	X
GeneMark	2012.04	[67]	Biology, Genomics, Metagenomics	X
Genewise	2.2.3	[68]	Biology, Genomics, Annotation	X
GMAP	20070928, 20120524, 20120612	[69]	Biology, Genomics	X
Grace	5.1.22	[70]	Graphics, plotting, 2D	X
Gromacs	4.0.4, 4.0.7	[71]	Physics, Modeling	X
HDF5	1.8.7, 1.8.8	[72]	Library, Data	X
HMMER3	3.0	[73]	Biology, Genomics	X
HTSeq	0.5.3p3	[74]	Biology, NGS	X
HugeSeq	1.0.1	[75]	Biology, NGS, Genomics	X
hypre	2.8.0	[76]	Library, Math, Physics	X
IM and IMa	2009.12.17	[77]	Biology, Population	X
IMa2	8.26.11	[78]	Biology, Population	X
Inelastica	1.1 (python/2.7.2)	[79]	Quantum Chemistry	X
IE3D	15.1	[80]	Simulation, Design	X
JDK	1.6.0_12, 1.7.0	[81]	Java Development Kit	X
Khmer	20120321	[82]	Biology, NGS, Utilities	X
Kmer	r1909	[83]	Biology, NGS, genome alignment	X
lammps	17-Sept11	[84]	Simulation	X
Last	193	[85]	Biology, Sequence alignment	X
libxc	1.1.0	[86]	Math, funtionals	X
MACS	1.4.1	[87]	Biology, ChIP-Seq	X
madness	1769	[88]	Math, DIff. Equation solving	X
mafft	6.859	[89]	Biology, Multiple sequence alignment	X
Maker	2.10	[90]	Biology, Annotation, Genomics	X
MapSplice	1.15.2	[91]	Biology, Genomics	X
Matlab	2009b	[92]	Math, Simulation, Programming	X
MATS	2.1.0	[93]	BIology, NGS	X
Mauve	2.3.1	[94]	Biology, Multiple genome alignments	X
MCL	11-335	[95]	Biology, Genomics, Clustering	X
meme	3.0.13, 4.3.0	[96]	Biology, Motifs, Sequence analysis	X
MetaPhyler	1.13	[97]	Biology, Metagenomics	X
metis	4.0	[98]	Math, Graph partitioning	X
Migrate-n	3.2.16	[99]	Biology, Population	X
mira	3.2.0, 3.4.0.1	[100]	Biology, NGS	X
mosaik	1.1.0021	[101]	Biology,NGS	X
MPIBlast	1.6.0	[102]	Biology, Sequence alignment	X
MrBayes	3.1.2,3.2.1	[103]	Biology, Phylogenetics	X
MUMmer	3.22	[104]	Biology, Genomics	X
MUSCLE	3.8.31	[105]	Biology, Genomics	X
NAMD	2.7b2	[106]	Simulation, Chemistry, Biology	X
NCO	4.0.9	[107]	Data exchange tools	X
netcdf	3.6.3, 4.1.2, 4.1.3	[108]	Data exchange, Tools	X
NetLogo	4.1.3	[109]	Modeling	X
Newbler	2.5.3, 2.6	[110]	Biology, NGS	X
NFFT	3.1.3	[111]	NDFT, library, math	X
Novoalign	2.07.15	[112]	Biology, NGS	X
NWChem	6.0	[113]	Simulation, Chemistry	X
Oases	0.2.04	[114]	Biology, NGS	X
OpenFOAM	1.7.1	[115]	Molecular Dynamics	X
OrthoMCL	2.0	[116]	Biology, Genomics	X
PAL2NAL	14	[117]	Biology, Genomics	X
PAML	4.4e	[118]	Biology, Phylogenetics	X
PAPI	4.1.2.1	[119]	CPU API	X
PASA	20110520	[120]	Biology, Genomics	X
PeakSplitter	1.0	[121]	Biology, Chip-Seq	X
PDT	3.16	[122]	Programming, Profiler	X
Perl	5.14.1	[123]	Programming, Language	X
PETSc	2.3.3-p8, 3.0.0-p12	[124]	MPI toolkit	X
Phred	020425	[125]	Biology, Genomics, Sequencing	X
PhyloBayes	3.3b	[126]	Biology, Phylogenetics	X
PhyML	3.0	[127]	Biology, Phylogenetics	X
Picard	1.54	[128]	Biology, NGS	X
Pindel	0.2.8	[129]	Biology, NGS	X
PQS	3.3-19	[130]	Modeling, Chemistry	X
Prinseq	0.17	[131]	Biology, NGS	X
PyOpenCL	2012.04	[132]	python, parallel programming	X
python	2.6.5, 2.7.2, 2.7.3	[133]	Programming, scripting, language	X	X
R	2.14.1, 2.14.1-MPI, 2.14.2	[134]	Statistics, Programming	X	X
RAxML	7.3.0	[135]	Biology, Phylogenetics	X
RAxML-Light	1.0.5	[136]	Biology, Phylogenetics	X
RepeatMasker	3.3.0	[137]	Biology, Genomics	X
Reptile	1.1, 1.1-omp	[138]	Biology, NGS, error correction	X
riboPicker	0.4.2	[139]	Biology, Sequence	X
Rosetta	2.1.1, 2.1.2	[140]	Biology, Structural, Modeling	X
Ruby	1.9.3	[141]	Programming, Language, Scripting	X
RSMToolkit	2961	[142]	Math, Modeling, Geometry	X
samtools	0.1.16, 0.1.18	[143]	Biology, NGS	X	X
SAS	9.2, 9.3	[144]	Statistics, Graphing	X	X
SATe	2.1.0	[145]	Biology, Phylogenetics	X
Scala	2.9.1	[146]	Programming, language, java	X
Segminator	0.0.2	[147]	Biology, NGS	X
SeqPrep	0.4	[148]	Biology, NGS	X
Siesta	2.0, 2.0.2, 3.0b	[149]	Simulation, physics, ab-initio	X
SOAPdenovo	1.05	[150]	Biology, NGS	X
SPARTA+	2.60	[151]	Chemistry	X
SRA	2.1.7	[152]]	biology, NGS	X	X
SRNAPredict	3.0	[153]	Biology, Genomics	X
SRNAScanner	200903	[154]	Biology, Genomics	X
Staden	2.0.0b9	[155]	Biology, Genomics, Sequencing	X	X
Stata	10	[156]	Statistics, Data analysis	X
Structure	2.3.3	[157]	Biology, Population	X
TAU	2.20.1	[158]	Profiling, Tracing, Programming	X
tgicl	2.1	[159]	Biology, sequencing, clustering	X
TRF	4.04	[160]	Biology, Genomics	X
Trimal	1.2	[161]	Biology, NGS	X
Trinity	r20120125, r20120317, r20120608	[162]	Biology, RNA-Seq	X
Tophat	1.3.0, 1.3.3, 1.4.1	[163]	Biology, NGS	X
tuxedo	The "tuxedo suite" - Bowtie, Tophat, and Cufflinks			X
Twinscan	3.5,4.1.2	[164]	Biology, Genomics	X
usearch	5.0.151,5.1.221	[165]	Biology, Sequence analysis	X
VASP	4.6.34,5.2.0	[166]	Quantum Chemistry, ab initio	X
VCFtools	0.1.7, 0.1.9	[167]	Biology, SNPs	X
velvet	1.2.06,1.2.02,1.2.01,1.1.05	[168]	Biology, NGS	X	X
vmd	1.9	[169]	Biology, Visualization	X
weka	3.6.2	[170]	Data mining algorithms	X
wgs	6.1, 6.1-20110830	[171]	Biology,Assembler,Genome	X
wublast	2.0	[172]	Biology, Sequence Alignment	X

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