An introductory list of bioinformatics software
commonly used in animal genomics research
- Sequence Analysis Software
- Base calling, assembling, viewing: Phred / Phrap / Consed
- SNP Analysis: Consed, DnaSP, PolyPhred, SNPidentifier, SNP PHAGE, SNPdetector, Consed,
- Alignment / Clustering: Arachne, Assembler, CAP3, ClustalW, ContigViewer, Exonerate, MultiAlin, PaCE, PCAP, Splign, Alignment Graphic Drawing
- Check low complexity: RepeatMasker, Repeatfinder
- RNAi searches: miRanda, MiRFinder, others
- Similarity Search: Blast, Blastz, Fasta, GMAP, Mulan, SynView, SynBrowse, ECR Browser, Others
- Primer design: Amplify, CodeHOP, Expeditor, OligoSpawn, FastPCR, Primer3, Primer Premier 5, Prim2,
- Next Gen Seq Analysis:
A list of next-gen-seq software
- Genome Analysis: Light weighted genome viewer, Vmatch
- Misc.: Reverse complement convertor, KegDraw,
- Genetics Analysis Software
- Linkage analysis: CarthaGene, Crimap, JoinMap, LocusMAP, Mapmaker, NCBI CONCORDE, RHMapper, Sibs, Locusmap, SCAT, HOTSPOTTER
- Haplotype analysis: fastPHASE, PHASE
- Genetics analysis: epiSNP, EPISNPmpi, MiNiInbred,
- QTL analysis: BmapQTL, MapQTL, QTL Cartographer, QTL Express, QTLBIM, Qxpak, PlabQTL, SPSSQTL, WebQTL, more ...
- Phylogeny analysis: Phylip, PAUP, PhyML, TimeTree, Eshadow, Others
- Pedigree: Pedigraph, Pedigree-Draw, MiniInbred, MORGAN (Monte Carlo Genetic Analysis, includes pedcheck, genedrop, etc.)
- Functional Genomics Software
- Domain/Motif Prediction: EST Scan, ORF Finder, ORFpredictor, Genome Scan, Pfam, PRINTS, PROSITE, Splice Predictor, more ...
- Gene Prediction: Augusrus, HMMgene, GENEscan, Grail, GLEAN, Jigsaw,
- Microarray Analysis: ArrayGenes, KegArray, HDB Stat, Power Atlas, more...,
- Genome analysis: GenomatiX, PepTool, Genewiz, Others (GeneScan, Genie, HMMGene).
- Gene Annotation and Analysis: Apollo, AmiGO, ENSMART, GoSurfer, GeneHopper, KegHier, CateGOrizer, GeneLynx, MatchMiner, Ontology On-line, Resourcerer, VisuaL Annotation Display
- Expressoin data analysis: DAVID and EASE, GenMAPP, Gaggle, Spotfire, TM4
- Comparative analysis: COGs, PEDANT 3, KEGG, TheSEED, GenDB, PUMA2
- Genetic Networks and System Biology
- Ontology: OBO Edit, COB Edit, Phenote, Protege Editor, Semantic Web,
- Software suites: SynBioSS, ToppGene Suite, GATACA, System Biology.ORG, Systems-Biology.ORG,
- General Applications
- Databases: AceDB, MySQL, PostgreSQL, Entrez Programming Utilities, perl DBI, PHP
- LIMS: Pipeline pilot, Progeny, more ...
- Packages:
EMBOSS (contains over 150 applications),
GMOD
(
Apollo,
CMap,
FlashGViewer,
GBrowse,
PubSearch,
TextPresso
)
BioMOBY,
BioRuby,
NCBI Tool Kit,
Biology WorkBench (SDSC)
- Programming Tools: BioPerl, BioJava
- Programmable Database Access:
EUtilities (NCBI),
Ensembl Perl API
Frequently used software manuals - Links:
Original list: December 15, 2003; Last updated: January 06, 2010; For new suggestions, send email to Zhiliang Hu
