Bioinformatics tools - Revision history

Christoph: /* Other tools */

2008-05-15T22:14:03Z

‎Other tools

Christoph: /* Other alignment tools */

2008-05-15T21:51:39Z

‎Other alignment tools

Christoph: /* Gene prediction tools */

2007-09-09T01:21:23Z

‎Gene prediction tools

Christoph at 02:23, 5 August 2007

2007-08-05T02:23:44Z

Christoph at 02:08, 27 June 2007

2007-06-27T02:08:53Z

Christoph at 02:03, 27 June 2007

2007-06-27T02:03:21Z

New page

==Multiple Sequence Alignment tools==
*[[Clustalw]]
*[[MUSCLE]]
*[[T-Coffee]]
*[[PROBCONS]]
*[[MAFFT]]
*[[AMAP]]
*[[Kalign]]
*[[Probalign]]
*[[Proda]]
===Whole Genome Multiple Alignment===
*[[PECAN]]
*[[MULTIZ]] and [[TBA]]
*[[LAGAN]], [[LAGAN#MLAGAN|MLAGAN]], [[LAGAN#SLAGAN|Shuffle LAGAN]]

==Pairwise alignment database searches==
*[[BLAST]]
**[[Module:Bio::Tools::Run::RemoteBlast]] (NCBI BLAST queue)
*[[FASTA alignment program|FASTA]]
*[[BLAT]]

==Other alignment tools==
*[[HMMER]] - [[wp:HMM|HMM]] 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
*[[FASTA|FASTX/Y]] - with SearchIO
*[[Sim4]]
*[[BLAT]]
*[[EST2genome]]
*[[Gmap]]
*[[Spidey]]

==[[Gene prediction]] tools==
*[[Genscan]]
*[[Genewise]]

* '''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 [[InParanoid#MultiParanoid|Multiparanoid]]
* [[MCL#TribeMCL|TribeMCL]]
* [[OrthoMCL]]
* [[Jaccard Clustering]]

==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====
* [[PHYLIP#ProtPars|ProtPars]] in [[PHYLIP]]
* [[PAUP]]
* [[LVB]]

====Distance====
* [[PHYLIP#Neighbor|Neighbor]] and [[PHYLIP#ProtDist|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)
* [[EMBOSS#distmat|distmat]] tool in [[EMBOSS]]
* [[Molphy]] - the [[Molphy#njdist|njdist]] app is part of Molphy

====Maximum Likelihood====
* [[PAUP]]
* [[Molphy]] - the [[Molphy#ProtML|ProtML]]
* [[Garli]]
* [[RAxML]]

====Bayesian====
* [[MrBayes]]
* [[BEAST]]
* [[BAMBE]]

===Molecular Evolution===
* [[PAML]] (Codeml, YN00, baseml, evolver)
* [http://darwin.uvigo.es/software/modeltest.html Modeltest] supported via Hyphy::Modeltest
* [http://www.hyphy.org 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
* [http://statgen.ncsu.edu/thorne/multidivtime.html Multidivtime] Jeff Thorne's divergence time estimator
* [[BEAST]]

===Rates of evolution===
* [[DART#Xgram|Xgram]] (xrate) <font color="red">not yet supported by Run</font>
* [http://compgen.bscb.cornell.edu/~acs/phastCons-HOWTO.html PhasCons]]

===Footprinting===
* [[Footprinter]] [http://wingless.cs.washington.edu/htbin-post/unrestricted/FootPrinterWeb/FootPrinterInput2.pl Footprinter webserver]

==Remote and local packages of applications==
* [[PISE]] - submit jobs to an external queue with hundreds of bioinformatics applications
* [http://emboss.sourceforge.net/ EMBOSS] - run these application locally
* [[EBI SOAP services]]

[[Category:Bioinformatics| ]]

← Older revision		Revision as of 02:23, 5 August 2007
Line 1:		Line 1:
		+	==/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]]

← Older revision		Revision as of 02:08, 27 June 2007
Line 149:		Line 149:
	* [[EBI SOAP services]]		* [[EBI SOAP services]]

		+	==External links==
		+	*[http://www.bioperl.org/wiki/Category:Tools BioPerl - Category:Tools]

	[[Category:Bioinformatics\| ]]		[[Category:Bioinformatics\| ]]

@@ Line 124: / Line 124: @@
 ==Other tools==
 *[[Primer3]] - primer predition
 *[[TribeMCL]] - gene family identification

@@ Line 71: / Line 71: @@
 ==Other alignment tools==
-*[[HMMER]] - [[wp:HMM|HMM]] based alignment
+*[[HMMER]] &mdash; [[wikipedia:Hidden Markov model|Hidden Markov model]] based alignment
 *[[Promoterwise]]
 *[[DBA]]

@@ Line 91: / Line 91: @@
 *[[Genscan]]
 *[[Genewise]]
+*[http://www.cbs.dtu.dk/services/EasyGene/ EasyGene 1.0 Server]
 * '''Wanted'''
 ** [[SNAP]] (writes [[GFF]] and [[ZFF]]) (this is pretty easy)