Bioinformatics tools

Multiple Sequence Alignment tools

• Clustalw
• MUSCLE
• T-Coffee
• PROBCONS
• MAFFT
• AMAP
• Kalign
• Probalign
• Proda

Whole Genome Multiple Alignment

• PECAN
• MULTIZ and TBA
• LAGAN, MLAGAN, Shuffle LAGAN

Pairwise alignment database searches

• BLAST
  • Module:Bio::Tools::Run::RemoteBlast (NCBI BLAST queue)
• FASTA
• BLAT

Other alignment tools

• HMMER - HMM based alignment
• Promoterwise
• DBA
• VISTA
• Profile

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

• Genscan
• Genewise

• 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-related tools

RNA motif prediction tools

• Infernal
• RNAMotif
• ERPIN
• tRNAscanSE

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

• InParanoid and Multiparanoid
• TribeMCL
• OrthoMCL
• Jaccard Clustering

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

• ProtPars in PHYLIP
• PAUP
• LVB

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

• PAUP
• Molphy - the ProtML
• Garli
• RAxML

Bayesian

• MrBayes
• BEAST
• BAMBE

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

• Xgram (xrate) not yet supported by Run
• PhasCons]

Footprinting

• Footprinter Footprinter webserver

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