Bioinformatics tools
From Christoph's Personal Wiki
Contents
- 1 Multiple Sequence Alignment tools
- 2 Pairwise alignment database searches
- 3 Other alignment tools
- 4 Protein and mRNA to genome (spliced) alignment tools
- 5 Gene prediction tools
- 6 RNA-related tools
- 7 Sequence family clustering and Orthology prediction
- 8 Other tools
- 9 Phylogenetics
- 10 Remote and local packages of applications
- 11 External links
Multiple Sequence Alignment tools
Whole Genome Multiple Alignment
Pairwise alignment database searches
- BLAST
- Module:Bio::Tools::Run::RemoteBlast (NCBI BLAST queue)
- FASTA
- BLAT
Other alignment tools
Protein and mRNA to genome (spliced) alignment tools
- Genewise - protein to genome
- Pseudowise - protein genome with frameshifts
- Exonerate - est2genome and protein2genome models as well as general models for sequence alignment
- FASTX/Y - with SearchIO
- Sim4
- BLAT
- EST2genome
- Gmap
- Spidey
Gene prediction tools
- Wanted
- SNAP (writes GFF and ZFF) (this is pretty easy)
- Twinscan (writes GFF )
- Genezilla (formerly TIGRScan) (writes GFF)
- GeneSplicer
- Glimmer and GlimmerHMM (parsers already written Bio::Tools::Glimmer)
- GeneMarkS
- SLAM
- ROSETTA
- ExonHunter
RNA motif prediction tools
RNA secondary structure prediction tools
- UNAFold (M. Zuker's unified replacement for mfold)
- Possibly the mfold utilities
- Vienna RNA tools
- Others?
Sequence family clustering and Orthology prediction
Other tools
- Primer3 - primer predition
- TribeMCL - gene family identification
- Prints
- Eponine
- FootPrinter
- SignalP
- TMHMM
- Coils
- RepeatMasker
- Mdust
- Seg
- Consense
- DrawGram
- DrawTree
- Phrap
- Profile
Phylogenetics
Reconstruction
Parsimony
Distance
- Neighbor and ProtDist tools in PHYLIP
- NJTree - this is also used for species tree and gene tree reconciliation in TreeFam
- Quicktree - fast NJ tree building (good for VERY large datasets)
- distmat tool in EMBOSS
- Molphy - the njdist app is part of Molphy
Maximum Likelihood
Bayesian
Molecular Evolution
- PAML (Codeml, YN00, baseml, evolver)
- Modeltest supported via Hyphy::Modeltest
- HyPhy Hyphy::SLAC, Hyphy::REL, Hyphy::FEL
Tree reconciliation
- Forester::SDI - speciation/duplication inference
- Softparsmap
- Notung
- Eulenstein
- GeneTree
- gtp
- primetv
- RAP
Divergence time estimation
- r8s - analysis of rates of evolution
- Multidivtime Jeff Thorne's divergence time estimator
- BEAST
Rates of evolution
Footprinting
Remote and local packages of applications
- PISE - submit jobs to an external queue with hundreds of bioinformatics applications
- EMBOSS - run these application locally
- EBI SOAP services
