- 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:
BWA,
BEDtools,
SeqTK,
SAM tools,
Shore,
SOPA,
TopHat ...
VCF utilities
(
BEAGLE |
VCF Tools |
Python VCF lib |
plink/seq),
more and
more
- Genome Analysis:
Light weighted genome viewer,
Vmatch
- Misc.:
Reverse complement convertor,
KegDraw,
- Genetics Analysis Software
- Linkage analysis:
CarthaGene
 ,
Cri-Map  ,
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,
Otterlace,
Resourcerer,
VisuaL Annotation Display
- Expressoin data analysis:
DAVID and EASE,
GenMAPP,
Gaggle,
Spotfire,
TM4,
UCSC Conservation Tracks,
ENCODE/,
Ensembl Compara
- Comparative analysis:
COGs,
DRIMM,
Ensembl Compara,
PEDANT 3,
KEGG,
TheSEED,
GenDB,
PUMA2,
VCmap
- Comparative Genomics Viewers:
Cmap,
CMap3D,
GBrowse_syn,
JBrowse,
Genome Projector,
Integrative Genomics Viewer,
Integrated Genome Browser,
SynBrowse,
Strudel,
VCMap
- 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,
Galaxy,
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:
- Canadian Bioinformatics Help Desk Software Repository
- NRSP-8 Animal Genomics Software Repository
- INRA Software Repository
- NIH Molecular Biology Software List
- ExPASy Proteomics Tools
(December 15, 2003 - August 25, 2020)
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