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,
ePCR,
mePCR,
MultiAlin,
PaCE,
PCAP,
Splign,
Alignment Graphic Drawing |
SSAHA,
MAQ,
Bowtie,
Mosaic,
- 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,
- Base calling, assembling, viewing:
Phred / Phrap / Consed
- 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.)
- Linkage analysis:
CarthaGene
- 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, Otterlace, 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,
- Trait/phenotype analysis: TASSEL (for Association Mapping)
- 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
(
CMap,
FlashGViewer,
GBrowse ,
PubSearch,
TextPresso
)
BioMOBY,
BioRuby,
NCBI Tool Kit,
Biology WorkBench (SDSC)
- Programming Tools: BioPerl, BioJava, R
- Programmable Database Access:
EUtilities (NCBI),
Ensembl Perl API
- Links to software resources:
Original list: December 15, 2003; Last updated: August 25, 2010; For new suggestions, send email to Zhiliang Hu
