Bioinformatics tools

From Christoph's Personal Wiki

/home/bin

Note: The following are some of my local bioinformatics-related utilities.

Directories

  • BOINC/
  • CCP4/
  • ciftr/
  • EMBOSS/
  • makefiles/
  • mpich2/ (parallel computing)
  • scripts/
  • SEALS/
  • Sirius/
  • validation/ (validate PDB format files)

Utilities

  • aausage.pl (see: Sequence logo)
  • agrep
  • chcase (+v2_chcase.pl)
  • clustalw / clustalw_help
  • describe
  • dict
  • dotter
  • fa2blc
  • gb2tab
  • getpdb
  • globin.pep
  • grepseq
  • matrix2png
  • molvolume
  • naccess
  • njplot
  • pdb2cif.awk / pdb2cif.pl
  • pdbcavity
  • pdbcm / pdbcm.awk
  • pdbinertia
  • pngcrush
  • ps2png.sh
  • pymol
  • rasmol / rasmol.hlp
  • resize_images
  • rmsfit / rmsfit-fast
  • roseplot
  • shawkle
  • superpose (aka SSM)
  • t_coffee
  • tex2im
  • transpose_csv.sh
  • wcseq
  • word_sort_count.pl

Multiple Sequence Alignment tools

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

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
  • EasyGene 1.0 Server
  • 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

  • MEME/MAST — motif discovery and search 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

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

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