Difference between revisions of "Bioinformatics tools"
From Christoph's Personal Wiki
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| + | ==/home/bin== | ||
| + | ''Note: The following are some of my local bioinformatics-related utilities.'' | ||
| + | ===Directories=== | ||
| + | *BOINC/ | ||
| + | *[[:Category:Ccp4|CCP4]]/ | ||
| + | *ciftr/ | ||
| + | *[[:Category:EMBOSS|EMBOSS]]/ | ||
| + | *[[make|makefiles]]/ | ||
| + | *mpich2/ (parallel computing) | ||
| + | *scripts/ | ||
| + | *[[:Category:SEALS|SEALS]]/ | ||
| + | *Sirius/ | ||
| + | *validation/ (validate PDB format files) | ||
| + | |||
| + | ===Utilities=== | ||
| + | *aausage.pl (see: [[Sequence logo]]) | ||
| + | *[[agrep]] | ||
| + | *[[chcase]] (+v2_chcase.pl) | ||
| + | *[[ClustalW|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== | ==Multiple Sequence Alignment tools== | ||
*[[Clustalw]] | *[[Clustalw]] | ||
| Line 21: | Line 71: | ||
==Other alignment tools== | ==Other alignment tools== | ||
| − | *[[HMMER]] | + | *[[HMMER]] — [[wikipedia:Hidden Markov model|Hidden Markov model]] based alignment |
*[[Promoterwise]] | *[[Promoterwise]] | ||
*[[DBA]] | *[[DBA]] | ||
| Line 41: | Line 91: | ||
*[[Genscan]] | *[[Genscan]] | ||
*[[Genewise]] | *[[Genewise]] | ||
| − | + | *[http://www.cbs.dtu.dk/services/EasyGene/ EasyGene 1.0 Server] | |
* '''Wanted''' | * '''Wanted''' | ||
** [[SNAP]] (writes [[GFF]] and [[ZFF]]) (this is pretty easy) | ** [[SNAP]] (writes [[GFF]] and [[ZFF]]) (this is pretty easy) | ||
| Line 74: | Line 124: | ||
==Other tools== | ==Other tools== | ||
| + | *[http://meme.sdsc.edu/meme/intro.html MEME/MAST] — motif discovery and search tools | ||
*[[Primer3]] - primer predition | *[[Primer3]] - primer predition | ||
*[[TribeMCL]] - gene family identification | *[[TribeMCL]] - gene family identification | ||
Latest revision as of 22:14, 15 May 2008
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
