Software-old: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
No edit summary
Line 11: Line 11:
! scope="col" | Website
! scope="col" | Website
! scope="col" | Category
! scope="col" | Category
! scope="col" | Cluster
|-
|-


|-
|-
| [[Blast|NCBI BLAST]] || 2.2.26 (+ and legacy) || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Bioinformatics
| [[454 Software]] || +version+ || +website+ || +category+ || +cluster+
|-
|-
| [[R]] || 2.15.0 || [http://www.r-project.org/] || Statistics
| [[aaarf]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ABySS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ABySS-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AlignACE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ALLPATHS-LG]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[amos]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AmpliconNoise]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ARB]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Artemis]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AUGUSTUS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AVID]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Bali-phy-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[bam2fastq]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BEAST]] || +version+ || +website+ || +category+ || +cluster+
|-
|-
| [[454 Software]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[aaarf]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ABySS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ABySS-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AlignACE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ALLPATHS-LG]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[amos]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AmpliconNoise]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ARB]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Artemis]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AUGUSTUS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[AVID]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Bali-phy-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[bam2fastq]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BEAST]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BEDTools]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BEST Bayesian]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BEST Binding]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BFast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Bioconductor]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BioPerl]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BioPython]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Bismark Bisulfite Mapper]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BiSS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Blastall]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Blat]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BMGE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[bowtie]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[bowtie2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[boxshade]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[breakdancer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[brownie]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[BS Seeker]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Burrows-Wheeler Aligner (BWA)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CAP3-rcluster IOB]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cd-hit]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cdbfasta]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CEAS]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CEGMA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CELLO]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[circos]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ClustalW]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Coding Potential Calculator]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Codon Usage]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CodonW]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CONSEL]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[consensus-v6c]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cortex_con]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cortex_var]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Count]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[count-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[CREST]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cufflinks]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[cutadapt]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[DLCoal]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ea-utils]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[edena]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[EMBOSS-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[emmix]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ESTScan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[evm (EVidenceModeler)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ExaML]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[exonerate]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FAR]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FAR (Flexible Adapter Remover)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FASTA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[fasta format cleaner]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FastQC]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[fasttree]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FastX]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FIRE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FitModel]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FLASH]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[FrameDP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GapFiller]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[gatk]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Gblocks]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Gblocks-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GCG (Wisconsin Package)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GeneMark]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Genezilla]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Genome]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GenomeMapper]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GenomeTools]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[gfftosam (BaseQV)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Glimmer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[GlimmerHMM]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[gmap]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[gmap-gsnap]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[go-perl]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[gpu-blast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Hmmer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[htseq]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[I-TASSER]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[IDEG]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[igb]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[IGV]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[IMa]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[indel-Seq-Gen]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[InStruct]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[inteRNA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[iParameterEstimation (iPE)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[iprscan (InterProScan)]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[iscan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Jellyfish]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[k-link]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[kaas]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[KiNG]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LAGAN]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LASTZ]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LDDist]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LDhat]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[libsequence]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LocARNA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[lsa]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[LUCY-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[macs]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[mafft]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[maker]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MAQ]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MaTogff]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MCL]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MCL-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MDscan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[megan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MEME]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MFOLD]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Migrate]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Minia]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MIRA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[miRanda]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[mosaik]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MOTHUR]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MOTHUR-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[mpiblast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MrBayes]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[mrfast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MSA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MSBlast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MSPcrunch]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Multiz]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MUMmer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MUSCLE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[mVISTA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[MyScanACE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NCBI Blast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NCBI Blast +]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ncbi blast parsers]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NCBI_database]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Newbler]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ngs_backbone]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NH PhyloBayes]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[nhPhyML]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NovelSeq]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[NovoAlign]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[nupack]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Oases]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[opal]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[OSPREY]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[p4]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pagan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PAML]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pandaseq]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Papara_nt]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PASHA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PeakSplitter]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pebl]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pfamDNASearch]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Pfam_scan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pftools]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[phred/phrap/conced]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PHYLIP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PhyloBayes]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PHYML]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[picard]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PIIM]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[plink]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PolyBayes-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pplacer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[prank]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[primegsr]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Primer3]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PrIMETV]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PSLDoc]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[PSORTb]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Pyrobayes,Mosaik,GigaBayes,]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[pysam]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Qiime]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Qiime-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[QTL Cartographer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[quake]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RactIP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RAxML]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RAxML-Light]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Ray]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RBR]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RCCBatchBlast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RECON]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RECON]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RepeatFinder]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Repeatmasker]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RepeatModeler]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RepeatScout]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Reputer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[riboPicker]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RMBlast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RNAz]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[rnnotator]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Roche]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RSAT]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RSEM]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[RUM]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[samtools]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SATé]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[scipio]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SeqClean]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SEQuel]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SHE-RA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SHORE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[shorha]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SHRIMP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[sickle]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SiZer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[slclust]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SNAP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[snowhite]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[snpEff]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SNVMix2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[soap2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SOAPdenovo]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SOAPdenovo-trans]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SOAPdenovo2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[socs]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SomaticCall]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[spaln]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[spimap]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SpliceGrapher]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[splign]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SRA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SSAHA2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SSPACE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[stacks]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[STAMP]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[STEM]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[strauto]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[structure]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SUPERSPLAT]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SVDetect]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[SVM_Light]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[T-Coffee]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[T-Coffee-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tabix]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tagdust]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Tandem Repeats Finder]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tassel]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tgicl]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[TIGER]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tophat]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[topHat-fusion-rcluster]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Tracer]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[TreeBeST]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[TreeView X]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[Trinity]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[tRNAscan-SE]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[twinScan/n-Scan]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[UNAFold]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[usearch]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[vcftools]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[velvet]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[VelvetOptimiser]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[ViennaRNA]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[vmatch]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[wcdest]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[wigToBigWig]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[WISE2]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[WU Blast]] || +version+ || +website+ || +category+ || +cluster+
|-
| [[yasra]] || +version+ || +website+ || +category+ || +cluster+
|-
 
|}
|}


Revision as of 12:10, 14 January 2013

Installed Software List

Last updated 2013-01-14.

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

Name Version Website Category Cluster
454 Software +version+ +website+ +category+ +cluster+
aaarf +version+ +website+ +category+ +cluster+
ABySS +version+ +website+ +category+ +cluster+
ABySS-rcluster +version+ +website+ +category+ +cluster+
AlignACE +version+ +website+ +category+ +cluster+
ALLPATHS-LG +version+ +website+ +category+ +cluster+
amos +version+ +website+ +category+ +cluster+
AmpliconNoise +version+ +website+ +category+ +cluster+
ARB +version+ +website+ +category+ +cluster+
Artemis +version+ +website+ +category+ +cluster+
AUGUSTUS +version+ +website+ +category+ +cluster+
AVID +version+ +website+ +category+ +cluster+
Bali-phy-rcluster +version+ +website+ +category+ +cluster+
bam2fastq +version+ +website+ +category+ +cluster+
BEAST +version+ +website+ +category+ +cluster+
454 Software +version+ +website+ +category+ +cluster+
aaarf +version+ +website+ +category+ +cluster+
ABySS +version+ +website+ +category+ +cluster+
ABySS-rcluster +version+ +website+ +category+ +cluster+
AlignACE +version+ +website+ +category+ +cluster+
ALLPATHS-LG +version+ +website+ +category+ +cluster+
amos +version+ +website+ +category+ +cluster+
AmpliconNoise +version+ +website+ +category+ +cluster+
ARB +version+ +website+ +category+ +cluster+
Artemis +version+ +website+ +category+ +cluster+
AUGUSTUS +version+ +website+ +category+ +cluster+
AVID +version+ +website+ +category+ +cluster+
Bali-phy-rcluster +version+ +website+ +category+ +cluster+
bam2fastq +version+ +website+ +category+ +cluster+
BEAST +version+ +website+ +category+ +cluster+
BEDTools +version+ +website+ +category+ +cluster+
BEST Bayesian +version+ +website+ +category+ +cluster+
BEST Binding +version+ +website+ +category+ +cluster+
BFast +version+ +website+ +category+ +cluster+
Bioconductor +version+ +website+ +category+ +cluster+
BioPerl +version+ +website+ +category+ +cluster+
BioPython +version+ +website+ +category+ +cluster+
Bismark Bisulfite Mapper +version+ +website+ +category+ +cluster+
BiSS +version+ +website+ +category+ +cluster+
Blastall +version+ +website+ +category+ +cluster+
Blat +version+ +website+ +category+ +cluster+
BMGE +version+ +website+ +category+ +cluster+
bowtie +version+ +website+ +category+ +cluster+
bowtie2 +version+ +website+ +category+ +cluster+
boxshade +version+ +website+ +category+ +cluster+
breakdancer +version+ +website+ +category+ +cluster+
brownie +version+ +website+ +category+ +cluster+
BS Seeker +version+ +website+ +category+ +cluster+
Burrows-Wheeler Aligner (BWA) +version+ +website+ +category+ +cluster+
CAP3-rcluster IOB +version+ +website+ +category+ +cluster+
cd-hit +version+ +website+ +category+ +cluster+
cdbfasta +version+ +website+ +category+ +cluster+
CEAS +version+ +website+ +category+ +cluster+
CEGMA +version+ +website+ +category+ +cluster+
CELLO +version+ +website+ +category+ +cluster+
circos +version+ +website+ +category+ +cluster+
ClustalW +version+ +website+ +category+ +cluster+
Coding Potential Calculator +version+ +website+ +category+ +cluster+
Codon Usage +version+ +website+ +category+ +cluster+
CodonW +version+ +website+ +category+ +cluster+
CONSEL +version+ +website+ +category+ +cluster+
consensus-v6c +version+ +website+ +category+ +cluster+
cortex_con +version+ +website+ +category+ +cluster+
cortex_var +version+ +website+ +category+ +cluster+
Count +version+ +website+ +category+ +cluster+
count-rcluster +version+ +website+ +category+ +cluster+
CREST +version+ +website+ +category+ +cluster+
cufflinks +version+ +website+ +category+ +cluster+
cutadapt +version+ +website+ +category+ +cluster+
DLCoal +version+ +website+ +category+ +cluster+
ea-utils +version+ +website+ +category+ +cluster+
edena +version+ +website+ +category+ +cluster+
EMBOSS-rcluster +version+ +website+ +category+ +cluster+
emmix +version+ +website+ +category+ +cluster+
ESTScan +version+ +website+ +category+ +cluster+
evm (EVidenceModeler) +version+ +website+ +category+ +cluster+
ExaML +version+ +website+ +category+ +cluster+
exonerate +version+ +website+ +category+ +cluster+
FAR +version+ +website+ +category+ +cluster+
FAR (Flexible Adapter Remover) +version+ +website+ +category+ +cluster+
FASTA +version+ +website+ +category+ +cluster+
fasta format cleaner +version+ +website+ +category+ +cluster+
FastQC +version+ +website+ +category+ +cluster+
fasttree +version+ +website+ +category+ +cluster+
FastX +version+ +website+ +category+ +cluster+
FIRE +version+ +website+ +category+ +cluster+
FitModel +version+ +website+ +category+ +cluster+
FLASH +version+ +website+ +category+ +cluster+
FrameDP +version+ +website+ +category+ +cluster+
GapFiller +version+ +website+ +category+ +cluster+
gatk +version+ +website+ +category+ +cluster+
Gblocks +version+ +website+ +category+ +cluster+
Gblocks-rcluster +version+ +website+ +category+ +cluster+
GCG (Wisconsin Package) +version+ +website+ +category+ +cluster+
GeneMark +version+ +website+ +category+ +cluster+
Genezilla +version+ +website+ +category+ +cluster+
Genome +version+ +website+ +category+ +cluster+
GenomeMapper +version+ +website+ +category+ +cluster+
GenomeTools +version+ +website+ +category+ +cluster+
gfftosam (BaseQV) +version+ +website+ +category+ +cluster+
Glimmer +version+ +website+ +category+ +cluster+
GlimmerHMM +version+ +website+ +category+ +cluster+
gmap +version+ +website+ +category+ +cluster+
gmap-gsnap +version+ +website+ +category+ +cluster+
go-perl +version+ +website+ +category+ +cluster+
gpu-blast +version+ +website+ +category+ +cluster+
Hmmer +version+ +website+ +category+ +cluster+
htseq +version+ +website+ +category+ +cluster+
I-TASSER +version+ +website+ +category+ +cluster+
IDEG +version+ +website+ +category+ +cluster+
igb +version+ +website+ +category+ +cluster+
IGV +version+ +website+ +category+ +cluster+
IMa +version+ +website+ +category+ +cluster+
indel-Seq-Gen +version+ +website+ +category+ +cluster+
InStruct +version+ +website+ +category+ +cluster+
inteRNA +version+ +website+ +category+ +cluster+
iParameterEstimation (iPE) +version+ +website+ +category+ +cluster+
iprscan (InterProScan) +version+ +website+ +category+ +cluster+
iscan +version+ +website+ +category+ +cluster+
Jellyfish +version+ +website+ +category+ +cluster+
k-link +version+ +website+ +category+ +cluster+
kaas +version+ +website+ +category+ +cluster+
KiNG +version+ +website+ +category+ +cluster+
LAGAN +version+ +website+ +category+ +cluster+
LASTZ +version+ +website+ +category+ +cluster+
LDDist +version+ +website+ +category+ +cluster+
LDhat +version+ +website+ +category+ +cluster+
libsequence +version+ +website+ +category+ +cluster+
LocARNA +version+ +website+ +category+ +cluster+
lsa +version+ +website+ +category+ +cluster+
LUCY-rcluster +version+ +website+ +category+ +cluster+
macs +version+ +website+ +category+ +cluster+
mafft +version+ +website+ +category+ +cluster+
maker +version+ +website+ +category+ +cluster+
MAQ +version+ +website+ +category+ +cluster+
MaTogff +version+ +website+ +category+ +cluster+
MCL +version+ +website+ +category+ +cluster+
MCL-rcluster +version+ +website+ +category+ +cluster+
MDscan +version+ +website+ +category+ +cluster+
megan +version+ +website+ +category+ +cluster+
MEME +version+ +website+ +category+ +cluster+
MFOLD +version+ +website+ +category+ +cluster+
Migrate +version+ +website+ +category+ +cluster+
Minia +version+ +website+ +category+ +cluster+
MIRA +version+ +website+ +category+ +cluster+
miRanda +version+ +website+ +category+ +cluster+
mosaik +version+ +website+ +category+ +cluster+
MOTHUR +version+ +website+ +category+ +cluster+
MOTHUR-rcluster +version+ +website+ +category+ +cluster+
mpiblast +version+ +website+ +category+ +cluster+
MrBayes +version+ +website+ +category+ +cluster+
mrfast +version+ +website+ +category+ +cluster+
MSA +version+ +website+ +category+ +cluster+
MSBlast +version+ +website+ +category+ +cluster+
MSPcrunch +version+ +website+ +category+ +cluster+
Multiz +version+ +website+ +category+ +cluster+
MUMmer +version+ +website+ +category+ +cluster+
MUSCLE +version+ +website+ +category+ +cluster+
mVISTA +version+ +website+ +category+ +cluster+
MyScanACE +version+ +website+ +category+ +cluster+
NCBI Blast +version+ +website+ +category+ +cluster+
NCBI Blast + +version+ +website+ +category+ +cluster+
ncbi blast parsers +version+ +website+ +category+ +cluster+
NCBI_database +version+ +website+ +category+ +cluster+
Newbler +version+ +website+ +category+ +cluster+
ngs_backbone +version+ +website+ +category+ +cluster+
NH PhyloBayes +version+ +website+ +category+ +cluster+
nhPhyML +version+ +website+ +category+ +cluster+
NovelSeq +version+ +website+ +category+ +cluster+
NovoAlign +version+ +website+ +category+ +cluster+
nupack +version+ +website+ +category+ +cluster+
Oases +version+ +website+ +category+ +cluster+
opal +version+ +website+ +category+ +cluster+
OSPREY +version+ +website+ +category+ +cluster+
p4 +version+ +website+ +category+ +cluster+
pagan +version+ +website+ +category+ +cluster+
PAML +version+ +website+ +category+ +cluster+
pandaseq +version+ +website+ +category+ +cluster+
Papara_nt +version+ +website+ +category+ +cluster+
PASHA +version+ +website+ +category+ +cluster+
PeakSplitter +version+ +website+ +category+ +cluster+
pebl +version+ +website+ +category+ +cluster+
pfamDNASearch +version+ +website+ +category+ +cluster+
Pfam_scan +version+ +website+ +category+ +cluster+
pftools +version+ +website+ +category+ +cluster+
phred/phrap/conced +version+ +website+ +category+ +cluster+
PHYLIP +version+ +website+ +category+ +cluster+
PhyloBayes +version+ +website+ +category+ +cluster+
PHYML +version+ +website+ +category+ +cluster+
picard +version+ +website+ +category+ +cluster+
PIIM +version+ +website+ +category+ +cluster+
plink +version+ +website+ +category+ +cluster+
PolyBayes-rcluster +version+ +website+ +category+ +cluster+
pplacer +version+ +website+ +category+ +cluster+
prank +version+ +website+ +category+ +cluster+
primegsr +version+ +website+ +category+ +cluster+
Primer3 +version+ +website+ +category+ +cluster+
PrIMETV +version+ +website+ +category+ +cluster+
PSLDoc +version+ +website+ +category+ +cluster+
PSORTb +version+ +website+ +category+ +cluster+
Pyrobayes,Mosaik,GigaBayes, +version+ +website+ +category+ +cluster+
pysam +version+ +website+ +category+ +cluster+
Qiime +version+ +website+ +category+ +cluster+
Qiime-rcluster +version+ +website+ +category+ +cluster+
QTL Cartographer +version+ +website+ +category+ +cluster+
quake +version+ +website+ +category+ +cluster+
RactIP +version+ +website+ +category+ +cluster+
RAxML +version+ +website+ +category+ +cluster+
RAxML-Light +version+ +website+ +category+ +cluster+
Ray +version+ +website+ +category+ +cluster+
RBR +version+ +website+ +category+ +cluster+
RCCBatchBlast +version+ +website+ +category+ +cluster+
RECON +version+ +website+ +category+ +cluster+
RECON +version+ +website+ +category+ +cluster+
RepeatFinder +version+ +website+ +category+ +cluster+
Repeatmasker +version+ +website+ +category+ +cluster+
RepeatModeler +version+ +website+ +category+ +cluster+
RepeatScout +version+ +website+ +category+ +cluster+
Reputer +version+ +website+ +category+ +cluster+
riboPicker +version+ +website+ +category+ +cluster+
RMBlast +version+ +website+ +category+ +cluster+
RNAz +version+ +website+ +category+ +cluster+
rnnotator +version+ +website+ +category+ +cluster+
Roche +version+ +website+ +category+ +cluster+
RSAT +version+ +website+ +category+ +cluster+
RSEM +version+ +website+ +category+ +cluster+
RUM +version+ +website+ +category+ +cluster+
samtools +version+ +website+ +category+ +cluster+
SATé +version+ +website+ +category+ +cluster+
scipio +version+ +website+ +category+ +cluster+
SeqClean +version+ +website+ +category+ +cluster+
SEQuel +version+ +website+ +category+ +cluster+
SHE-RA +version+ +website+ +category+ +cluster+
SHORE +version+ +website+ +category+ +cluster+
shorha +version+ +website+ +category+ +cluster+
SHRIMP +version+ +website+ +category+ +cluster+
sickle +version+ +website+ +category+ +cluster+
SiZer +version+ +website+ +category+ +cluster+
slclust +version+ +website+ +category+ +cluster+
SNAP +version+ +website+ +category+ +cluster+
snowhite +version+ +website+ +category+ +cluster+
snpEff +version+ +website+ +category+ +cluster+
SNVMix2 +version+ +website+ +category+ +cluster+
soap2 +version+ +website+ +category+ +cluster+
SOAPdenovo +version+ +website+ +category+ +cluster+
SOAPdenovo-trans +version+ +website+ +category+ +cluster+
SOAPdenovo2 +version+ +website+ +category+ +cluster+
socs +version+ +website+ +category+ +cluster+
SomaticCall +version+ +website+ +category+ +cluster+
spaln +version+ +website+ +category+ +cluster+
spimap +version+ +website+ +category+ +cluster+
SpliceGrapher +version+ +website+ +category+ +cluster+
splign +version+ +website+ +category+ +cluster+
SRA +version+ +website+ +category+ +cluster+
SSAHA2 +version+ +website+ +category+ +cluster+
SSPACE +version+ +website+ +category+ +cluster+
stacks +version+ +website+ +category+ +cluster+
STAMP +version+ +website+ +category+ +cluster+
STEM +version+ +website+ +category+ +cluster+
strauto +version+ +website+ +category+ +cluster+
structure +version+ +website+ +category+ +cluster+
SUPERSPLAT +version+ +website+ +category+ +cluster+
SVDetect +version+ +website+ +category+ +cluster+
SVM_Light +version+ +website+ +category+ +cluster+
T-Coffee +version+ +website+ +category+ +cluster+
T-Coffee-rcluster +version+ +website+ +category+ +cluster+
tabix +version+ +website+ +category+ +cluster+
tagdust +version+ +website+ +category+ +cluster+
Tandem Repeats Finder +version+ +website+ +category+ +cluster+
tassel +version+ +website+ +category+ +cluster+
tgicl +version+ +website+ +category+ +cluster+
TIGER +version+ +website+ +category+ +cluster+
tophat +version+ +website+ +category+ +cluster+
topHat-fusion-rcluster +version+ +website+ +category+ +cluster+
Tracer +version+ +website+ +category+ +cluster+
TreeBeST +version+ +website+ +category+ +cluster+
TreeView X +version+ +website+ +category+ +cluster+
Trinity +version+ +website+ +category+ +cluster+
tRNAscan-SE +version+ +website+ +category+ +cluster+
twinScan/n-Scan +version+ +website+ +category+ +cluster+
UNAFold +version+ +website+ +category+ +cluster+
usearch +version+ +website+ +category+ +cluster+
vcftools +version+ +website+ +category+ +cluster+
velvet +version+ +website+ +category+ +cluster+
VelvetOptimiser +version+ +website+ +category+ +cluster+
ViennaRNA +version+ +website+ +category+ +cluster+
vmatch +version+ +website+ +category+ +cluster+
wcdest +version+ +website+ +category+ +cluster+
wigToBigWig +version+ +website+ +category+ +cluster+
WISE2 +version+ +website+ +category+ +cluster+
WU Blast +version+ +website+ +category+ +cluster+
yasra +version+ +website+ +category+ +cluster+

Computational Chemistry

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=Software-old&oldid=366"