Bioinformatics tools extracted from a typical mammalian genome project [supplement]

This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to keep in the post, but I wanted it to be web-searchable. A copy also resides at FigShare: http://dx.doi.org/10.6084/m9.figshare.1194867

Software tool/object/item/resource access site reference if available main paper?
ABC Approximate Bayesian Computation none named, provided yet Veeramah et al, submitted yes
ARACHNE http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page http://genomebiology.com/content/10/8/R88 yes
AWTY (Are We There Yet?) http://ceb.scs.fsu.edu/awty http://bioinformatics.oxfordjournals.org/content/24/4/581.long
axtChain http://genomewiki.ucsc.edu/index.php/The_source_tree http://www.pnas.org/content/100/20/11484.long
Baylor College of Medicine gibbon genome project https://www.hgsc.bcm.edu/gibbon-genome-project yes
BEAST https://code.google.com/p/beast-mcmc/ http://www.biomedcentral.com/1471-2148/7/214 yes
BEDOPS https://github.com/bedops/bedops http://www.ncbi.nlm.nih.gov/pubmed/22576172
BEDtools https://github.com/arq5x/bedtools2 http://www.ncbi.nlm.nih.gov/pubmed/20110278
BioCarta http://www.biocarta.com/ can’t find citation
BioCyc http://biocyc.org/ http://www.ncbi.nlm.nih.gov/pubmed/16246909
BioEdit http://www.mbio.ncsu.edu/bioedit/bioedit.html can’t find citation
bl2seq http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq http://www.ncbi.nlm.nih.gov/pubmed/18440982
BLAST http://blast.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/pubmed/2231712
blastn http://blast.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/pubmed/2231712
BLASTZ http://www.bx.psu.edu/miller_lab/ http://genome.cshlp.org/content/13/1/103.long
BLAT http://genome.ucsc.edu/cgi-bin/hgBlat?command=start http://www.ncbi.nlm.nih.gov/pubmed/11932250
Bowtie 2 http://bowtie-bio.sourceforge.net/index.shtml http://www.ncbi.nlm.nih.gov/pubmed/19261174
BWA http://bio-bwa.sourceforge.net/ http://www.ncbi.nlm.nih.gov/pubmed/19451168
CAFE 3.0 http://www.bio.indiana.edu/~hahnlab/Software.html http://www.ncbi.nlm.nih.gov/pubmed/23709260
CCAT http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm http://www.ncbi.nlm.nih.gov/pubmed/20371496
CEGMA http://korflab.ucdavis.edu/Datasets/cegma/ http://www.ncbi.nlm.nih.gov/pubmed/17332020
chainNet http://genomewiki.ucsc.edu/index.php/Chains_Nets http://www.ncbi.nlm.nih.gov/pubmed/14500911
CleanSam http://samtools.sourceforge.net/ http://www.ncbi.nlm.nih.gov/pubmed/19505943
closestBed see BEDTools http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
ClustalW http://www.clustal.org/clustal2/ http://www.ncbi.nlm.nih.gov/pubmed/17846036
ConsensusPathwayDB (CPDB) http://consensuspathdb.org/ http://www.ncbi.nlm.nih.gov/pubmed/23143270 yes
Coseg http://www.repeatmasker.org/COSEGDownload.html can’t find citation
cross_match http://www.phrap.org/phredphrapconsed.html#block_phrap http://www.ncbi.nlm.nih.gov/pubmed/9521921
cross-species array CGH much software http://www.ncbi.nlm.nih.gov/pubmed/17666543
cutadapt https://code.google.com/p/cutadapt/ http://journal.embnet.org/index.php/embnetjournal/article/view/200
DAVID http://david.abcc.ncifcrf.gov/ http://www.ncbi.nlm.nih.gov/pubmed/19131956 yes
DNAsp 5.10.1 http://www.ub.edu/dnasp http://www.ncbi.nlm.nih.gov/pubmed/19346325
DUST http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker/ http://www.ncbi.nlm.nih.gov/pubmed/16796549
eHIVE pipeline http://www.ensembl.org/info/docs/eHive/index.html http://www.ncbi.nlm.nih.gov/pubmed/20459813
ENSEMBL http://www.ensembl.org/ http://www.ncbi.nlm.nih.gov/pubmed/24316576 yes
ENSEMBL annotation pipeline http://www.ensembl.org/info/genome/genebuild/genome_annotation.html https://github.com/Ensembl
ENSEMBL COMPARA http://useast.ensembl.org/info/genome/compara/index.html https://github.com/Ensembl/ensembl-compara
ENSEMBL RNA-seq pipeline http://www.ensembl.org/info/genome/genebuild/rnaseq_annotation.html http://www.ncbi.nlm.nih.gov/pubmed/22798491
Eponin-scan https://www.sanger.ac.uk/resources/software/eponine/ http://www.ncbi.nlm.nih.gov/pubmed/11875034
European Nucleotide Archive http://www.ebi.ac.uk/ena/ http://www.ncbi.nlm.nih.gov/pubmed/24214989
Exonerate https://www.ebi.ac.uk/~guy/exonerate/ http://www.biomedcentral.com/1471-2105/6/31
FASTQ http://maq.sourceforge.net/fastq.shtml http://www.ncbi.nlm.nih.gov/pubmed/20015970
FigTree http://tree.bio.ed.ac.uk/software/figtree/ http://figtree.googlecode.com/
FirstEF http://rulai.cshl.org/tools/FirstEF/ http://www.ncbi.nlm.nih.gov/pubmed/11726928
FISH data http://www.biologia.uniba.it/gibbon http://www.ncbi.nlm.nih.gov/pubmed/25209798
GARLI https://www.nescent.org/wg_garli/Main_Page http://molevol.lysine.umiacs.umd.edu/molevolfiles/garli/zwicklDissertation.pdf
GATK https://www.broadinstitute.org/gatk/ http://www.ncbi.nlm.nih.gov/pubmed/20644199
GATK UnifiedGenotyper see GATK
Gblocks http://molevol.cmima.csic.es/castresana/Gblocks.html http://www.ncbi.nlm.nih.gov/pubmed/10742046
GenBank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/pubmed/23193287 yes
Gene Ontology http://www.geneontology.org/ http://www.ncbi.nlm.nih.gov/pubmed/10802651 yes
GeneBuilder https://github.com/sanger-pathogens/Artemis/blob/master/uk/ac/sanger/artemis/components/genebuilder/BasicGeneBuilderFrame.java http://www.ncbi.nlm.nih.gov/pubmed/10487869
Geneious 5.6.5 http://www.geneious.com/ can’t find citation
GeneMANIA http://www.genemania.org/ http://www.ncbi.nlm.nih.gov/pubmed/23794635 yes
GeneTree pipeline (Ensembl) http://www.ensembl.org/info/genome/compara/homology_method.html says Beal, in prep
Genewise http://www.ebi.ac.uk/Tools/psa/genewise/help/ http://www.ncbi.nlm.nih.gov/pubmed/15123596
Genome Reference Consortium http://genomereference.org/ www.ncbi.nlm.nih.gov/pubmed/21750661
Genscan http://genes.mit.edu/GENSCAN.html www.ncbi.nlm.nih.gov/pubmed/9149143
Goslim http://geneontology.org/page/go-slim-and-subset-guide http://www.ncbi.nlm.nih.gov/pubmed/10802651 yes
GOTERM_BP_FAT see DAVID
GOTERM_CC_FAT see DAVID
GOTERM_MF_FAT see DAVID
G-PhosCS http://compgen.bscb.cornell.edu/GPhoCS/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245873/ yes
Hapsembler http://compbio.cs.toronto.edu/hapsembler/ http://link.springer.com/chapter/10.1007%2F978-3-642-20036-6_5
hcluster_sg http://treesoft.svn.sourceforge.net/viewvc/treesoft/branches/lh3/hcluster/
HMMer 3.0 http://hmmer.janelia.org/ www.ncbi.nlm.nih.gov/pubmed/22039361
IGV Integrative Genomics Viewer http://www.broadinstitute.org/igv/ www.ncbi.nlm.nih.gov/pubmed/21221095 yes
INOH http://inoh.hgc.jp/ Satoko Sakai, Noriko Sakai, Hiromi Nakamura, Ken Fukuda, Toshihisa Takagi. 2009. INOH Pathway Database. MBSJ 2009 (The 32nd Annual Meeting of the Molecular Biology Society of Japan).
in-silico PCR http://users.soe.ucsc.edu/~kent/src/ http://www.ncbi.nlm.nih.gov/pubmed/24270787
jModeltest https://code.google.com/p/jmodeltest2/ www.ncbi.nlm.nih.gov/pubmed/22847109
KEGG http://www.kegg.jp/ http://www.ncbi.nlm.nih.gov/pubmed/24214961
LASTZ http://www.bx.psu.edu/~rsharris/lastz/ http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf
LiftOver http://genome.ucsc.edu/cgi-bin/hgLiftOver http://www.ncbi.nlm.nih.gov/pubmed/24270787
LogCombiner http://beast.bio.ed.ac.uk/logcombiner http://www.ncbi.nlm.nih.gov/pubmed/22367748
MAFFT http://mafft.cbrc.jp/alignment/software/ www.ncbi.nlm.nih.gov/pubmed/23329690
maximum likelihood method none named, provided http://www.ncbi.nlm.nih.gov/pubmed/19379804
M-Coffee http://www.tcoffee.org/ www.ncbi.nlm.nih.gov/pubmed/16556910
MEGA 5 www.megasoftware.net http://www.ncbi.nlm.nih.gov/pubmed/21546353
MEGABLAST http://blast.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/pubmed/18567917
mergeBED see BEDTools http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
MrBayes http://mrbayes.sourceforge.net/ www.ncbi.nlm.nih.gov/pubmed/11743192
mrFAST http://sourceforge.net/projects/mrfast/files/mrfast/ www.ncbi.nlm.nih.gov/pubmed/19718026
mrsFAST http://mrsfast.sourceforge.net/Home www.ncbi.nlm.nih.gov/pubmed/20676076
ms http://home.uchicago.edu/~rhudson1/source/mksamples.html http://www.ncbi.nlm.nih.gov/pubmed/11847089
multiz http://www.bx.psu.edu/miller_lab/ http://www.ncbi.nlm.nih.gov/pubmed/15060014
multtest package in R http://www.bioconductor.org/packages/release/bioc/html/multtest.html http://link.springer.com/chapter/10.1007/0-387-29362-0_15
MUSCLE http://www.drive5.com/muscle/ http://www.ncbi.nlm.nih.gov/pubmed/15034147
NCBI http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/pubmed/24259429 yes
NetPath http://www.netpath.org/ http://www.ncbi.nlm.nih.gov/pubmed/20067622
Network version 4.611 http://www.fluxus-engineering.com/sharenet.htm http://www.ncbi.nlm.nih.gov/pubmed/10331250
Oxford plots R script by a paper author no citation yes
PAML http://abacus.gene.ucl.ac.uk/software/paml.html http://www.ncbi.nlm.nih.gov/pubmed/17483113
paralogs vs orthologs http://www.soe.ucsc.edu/~kent http://www.ncbi.nlm.nih.gov/pubmed/14500911
PathwayCommons http://www.pathwaycommons.org/ http://www.ncbi.nlm.nih.gov/pubmed/21071392
PAUP* http://paup.csit.fsu.edu/ http://paup.csit.fsu.edu/about.html
permutation testing https://github.com/cwhelan/permuting-feature-enrichment-test no citation
Phrap http://www.phrap.org Green P. 1996. Phrap documentation.
phred http://www.phrap.org/phredphrapconsed.html http://www.ncbi.nlm.nih.gov/pubmed/9521921
PHYLIP http://evolution.genetics.washington.edu/phylip.html Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
phylofit http://compgen.bscb.cornell.edu/phast www.ncbi.nlm.nih.gov/pubmed/21278375
Picard v 1.70 http://broadinstitute.github.io/picard/ A: Currently there is no Picard paper. You can cite Picard by referring to the website
PicardMergSamFiles see Picard
PID http://pid.nci.nih.gov/ http://www.ncbi.nlm.nih.gov/pubmed/18832364
Pmatch http://www.bioperl.org/wiki/PMATCH R. Durbin, unpublished
Primer3 http://bioinfo.ut.ee/primer3/ http://www.ncbi.nlm.nih.gov/pubmed/17379693
PRSF see MrBayes
PSMC https://github.com/lh3/psmc www.ncbi.nlm.nih.gov/pubmed/19505943 yes
pybedtools https://pypi.python.org/pypi/pybedtools http://www.ncbi.nlm.nih.gov/pubmed/21949271
QuickTree http://www.sanger.ac.uk/resources/software/quicktree/ http://www.ncbi.nlm.nih.gov/pubmed/12424131
randomBed http://bedtools.readthedocs.org/en/latest/content/tools/random.html
Reactome http://www.reactome.org/ http://www.ncbi.nlm.nih.gov/pubmed/24243840
RefSeq http://www.ncbi.nlm.nih.gov/refseq/ http://www.ncbi.nlm.nih.gov/pubmed/24259432
RepeatMasker http://www.repeatmasker.org Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0. 1996-2010 <http://www.repeatmasker.org>. yes
REVIGO http://revigo.irb.hr http://www.ncbi.nlm.nih.gov/pubmed/21789182 yes
rphast http://compgen.bscb.cornell.edu/rphast/ www.ncbi.nlm.nih.gov/pubmed/21278375
samtools http://www.htslib.org/ www.ncbi.nlm.nih.gov/pubmed/19505943
SAS/STAT http://www.sas.com/ SAS®/STAT software (PROC GLM), version 9.3, SAS System for Windows
Sequence Read Archive (aka short read archive) http://www.ncbi.nlm.nih.gov/sites/sra http://www.ncbi.nlm.nih.gov/pubmed/18045790 yes
Signalink http://signalink.org/ http://www.ncbi.nlm.nih.gov/pubmed/23331499
SMPDB http://www.smpdb.ca/ http://www.ncbi.nlm.nih.gov/pubmed/24203708
splitfa https://github.com/lh3/psmc/blob/master/utils/splitfa.c www.ncbi.nlm.nih.gov/pubmed/19505943
stampy http://www.well.ox.ac.uk/project-stampy http://www.ncbi.nlm.nih.gov/pubmed/20980556
TandemRepeatFinder (aka TRF) http://tandem.bu.edu/trf/trf.html http://www.ncbi.nlm.nih.gov/pubmed/9862982
TRACER http://beast.bio.ed.ac.uk/Tracer Rambaut A, Suchard MA, Xie D & Drummond AJ (2014) Tracer v1.6, Available from http://beast.bio.ed.ac.uk/Tracer
TreeAnnotator http://beast.bio.ed.ac.uk/treeannotator http://www.ncbi.nlm.nih.gov/pubmed/22367748
TreeBeST http://treesoft.sourceforge.net/treebest.shtml http://www.ncbi.nlm.nih.gov/pubmed/16381935
TreeMap (DrasticTreemap at REVIGO) http://www.drasticdata.nl/DrasticTreemapGApi/ http://www.ncbi.nlm.nih.gov/pubmed/21789182 yes
tRNAscan-SE http://lowelab.ucsc.edu/tRNAscan-SE/ http://www.ncbi.nlm.nih.gov/pubmed/9023104
UCSC Genome Browser http://genome.ucsc.edu http://www.ncbi.nlm.nih.gov/pubmed/24270787 yes
UniGene http://www.ncbi.nlm.nih.gov/unigene/ http://www.ncbi.nlm.nih.gov/pubmed/19910364
UniProt http://www.uniprot.org/ http://www.ncbi.nlm.nih.gov/pubmed/24253303
Wikipathways http://wikipathways.org/ http://www.ncbi.nlm.nih.gov/pubmed/22096230
WU-BLAST http://blast.wustl.edu/ http://www.ncbi.nlm.nih.gov/pubmed/2231712


Reference:

Carbone L., R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken & Fabio Anaclerio & (2014). Gibbon genome and the fast karyotype evolution of small apes, Nature, 513 (7517) 195-201. DOI: http://dx.doi.org/10.1038/nature13679