Bioinformatics tools

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Multiple Sequence Alignment tools

Whole Genome Multiple Alignment

Pairwise alignment database searches

Other alignment tools

Protein and mRNA to genome (spliced) alignment tools

Gene prediction tools

RNA-related tools

RNA motif prediction tools

RNA secondary structure prediction tools

Sequence family clustering and Orthology prediction

Other tools

Phylogenetics

Reconstruction

Parsimony

Distance

Maximum Likelihood

Bayesian

Molecular Evolution

  • PAML (Codeml, YN00, baseml, evolver)
  • Modeltest supported via Hyphy::Modeltest
  • HyPhy Hyphy::SLAC, Hyphy::REL, Hyphy::FEL

Tree reconciliation

Divergence time estimation

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

External links