- 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:
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