Bioinformatics tools
From Christoph's Personal Wiki
Contents
- 1 /home/bin
- 2 Multiple Sequence Alignment tools
- 3 Pairwise alignment database searches
- 4 Other alignment tools
- 5 Protein and mRNA to genome (spliced) alignment tools
- 6 Gene prediction tools
- 7 RNA-related tools
- 8 Sequence family clustering and Orthology prediction
- 9 Other tools
- 10 Phylogenetics
- 11 Remote and local packages of applications
- 12 External links
/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
Pairwise alignment database searches
- BLAST
- Module:Bio::Tools::Run::RemoteBlast (NCBI BLAST queue)
- FASTA
- BLAT
Other alignment tools
- HMMER — Hidden Markov model 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
- 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 motif prediction tools
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
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
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
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
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
