Run package
From BioPerl
(Redirected from Bioperl-run)
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:
You can download it by following the instructions on the Git page. The repository name is bioperl-run.
Multiple Sequence Alignment tools
- Clustalw
- MUSCLE
- T-Coffee
- PROBCONS
- MAFFT
- AMAP
- Kalign
- Probalign
- Proda
- Prank - not yet supported by Run
Whole Genome Multiple Alignment
- PECAN
- MULTIZ and TBA
- LAGAN, MLAGAN, Shuffle LAGAN
- MUMMER - not yet supported by Run
- MAUVE - not yet supported by Run
Pairwise alignment database searches
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 -- not yet supported
- 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
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
- 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
- A general interface to MCL; a number of the programs that come with MCL are Perl scripts, so conversion to BioPerl shouldn't be too hard.
- Other clustering algorithms
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/TreeBeST - this is also used for species tree and gene tree reconciliation in TreeFam
- Quicktree - fast NJ tree building (good for VERY large datasets)
- FastME - fast tree building based on minimum evolution (good for VERY large datasets) - not yet supported by Run
- distmat tool in EMBOSS
- Molphy - the njdist app is part of Molphy, not yet supported by Run
Maximum Likelihood
- Molphy - the ProtML
- Phyml
- PAML (Codeml, baseml)
- PAUP not yet supported by Run
- Garli not yet supported by Run
- RAxML not yet supported by Run
Bayesian
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
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
