Run package

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The BioPerl-Run package provides wrapper modules around many common bioinformatics applications and tools. In order to use it you must first install the core package.

The latest code

The latest, and not completely tested, code can be viewed here:

bioperl-run

You can download it by following the instructions on the Git page. The repository name is bioperl-run.

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

Support for the following have been added, except where noted. Others are planned if requested (QRNA, TransTerm, NAB, RNABOB, etc).

RNA secondary structure prediction tools

Note: These are not currently supported by Run; support will be added over time once an appropriate class system is in place

Sequence family clustering and Orthology prediction

Other tools

Phylogenetics

Reconstruction

Parsimony

Distance

Maximum Likelihood

Bayesian

  • MrBayes not yet supported by Run
  • BEAST not yet supported by Run
  • BAMBE not yet supported by Run

Molecular Evolution

  • PAML (Codeml, YN00, baseml, evolver)
  • SLR - Sitewise Likelihood Ratio software
  • Recodon - not yet supported by Run
  • HyPhy Hyphy::SLAC, Hyphy::REL, Hyphy::FEL
  • HyPhy Hyphy::F_ST - not yet supported by Run
  • Modeltest supported via Hyphy::Modeltest
  • VariScan - not yet supported by Run
  • Sweep - not yet supported by Run
  • HKA test - either using HKA or implemented in Module:Bio::PopGen - not yet supported by Run

Tree reconciliation

  • Forester::SDI - speciation/duplication inference not yet supported by Run
  • Softparsmap - not yet supported by Run
  • Notung - not yet supported by Run
  • Eulenstein - not yet supported by Run
  • GeneTree - not yet supported by Run
  • gtp - not yet supported by Run
  • primetv - not yet supported by Run
  • RAP - not yet supported by Run

(Thanks to Stefanie Hartmann for many of these links)

Divergence time estimation

  • r8s - analysis of rates of evolution not yet supported by Run
  • Multidivtime Jeff Thorne's divergence time estimator not yet supported by Run
  • BEAST

Rates of evolution

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

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
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