Difference between revisions of "Software"

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* Blast
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==Alignment==
* Fasta
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*[http://faculty.biomath.ucla.edu/msuchard/bali-phy/index.php Bali-Phy]
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*[ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/ BMGE]
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*[http://fsa.sourceforge.net/ FSA]
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*[http://molevol.cmima.csic.es/castresana/Gblocks.html Gblocks]
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*[http://guidance.tau.ac.il/ Guidance]
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*[http://www.jalview.org/ Jalview]
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*[http://mafft.cbrc.jp/alignment/software/ MAFFT]
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*[http://www.megasoftware.net/ MEGA]
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*[http://www.drive5.com/muscle/ MUSCLE]
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*[http://opal.cs.arizona.edu/ Opal]
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*[http://www.ebi.ac.uk/goldman-srv/prank/ PRANK]
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*[http://biowiki.org/bin/view/Main/ProtPal ProtPal]
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*[http://pbil.univ-lyon1.fr/software/seaview.html SeaView]
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*[http://www.tcoffee.org/ T-Coffee]
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==Phylogenetic tree building and analysis==
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* [http://www.beast2.org/ BEAST2] - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
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* [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST]
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* [http://pythonhosted.org/DendroPy/ DendroPy]
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* [http://phylo.bio.ku.edu/content/tracy-heath-dppdiv DPPDiv]
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*[http://www.microbesonline.org/fasttree/ FastTree]
 
* [http://tree.bio.ed.ac.uk/software/figtree/ FigTree]
 
* [http://tree.bio.ed.ac.uk/software/figtree/ FigTree]
* GARLI
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* [http://garli.googlecode.com/ Garli]
**[http://www.nescent.org/wg_garli/ Support page]
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**[[Garli_wiki | Documentation wiki ]]
**[http://garli.googlecode.com/ Program download]
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**[http://groups.google.com/group/garli_users/ Google users group]
**[http://phylo.bio.ku.edu/slides/GarliDemo/garliExercise.html Workshop tutorial]
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**[http://phylo.bio.ku.edu/slides/GarliDemo/garliExercise.WH2014.html Workshop tutorial] '''(NOTE: The tutorial bundle linked on this page contains everything you need - you don't need to download the program separately!)'''
* LAMARC: Demonstration and Tutorial on Augst 2nd ([[Peter Beerli]])
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* MP-EST
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** [http://code.google.com/p/mp-est/ Executables, code]
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** [http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/index.php Species tree web server]
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* [http://www.mrbayes.net MrBayes]
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* [http://statgen.ncsu.edu/thorne/multidivtime.html multidivtime]
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* [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
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* [http://phylosolutions.com/paup-test PAUP*]
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* [http://code.google.com/p/phybase/ PHYBASE]
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* [http://pbil.univ-lyon1.fr/software/phyldog/ PHYLDOG]
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* [http://www.phylobayes.org PhyloBayes]
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*[http://sco.h-its.org/exelixis/software.html RAxML (and many other programs)]
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* [http://sourceforge.net/projects/revbayes/ RevBayes]
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*[http://kiwi.cs.dal.ca/Software/RSPR rSPR]
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*[http://kiwi.cs.dal.ca/Software/SPRSupertrees SPRSupertrees]
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* [http://www.stat.osu.edu/~lkubatko/software/STEM/ STEM]
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* [http://tree.bio.ed.ac.uk/software/tracer/ Tracer]
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*[http://evolution.gs.washington.edu/phylip/software.html Comprehensive list of Phylogeny programs]
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==Other==
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* [http://people.sc.fsu.edu/~pbeerli/bugs_in_a_box.tar.gz Bugs in a Box]: A Macintosh program and its (python) source code to show the coalescence process (but still does not draw a tree).
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*[[Media:MCMCEG.zip | MCMC example software]] from [[John_Huelsenbeck | John Huelsenbeck]]
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* [http://ipyrad.readthedocs.io/ ipyrad]
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==Pipelines==
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*[https://bitbucket.org/caseywdunn/agalma Agalma]
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==Population analysis==
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* LAMARC: (If you want to know more about Lamarc talk to [[Peter Beerli]])
 
**[http://evolution.genetics.washington.edu/lamarc/index.html Lamarc] main website: Dowload and manual
 
**[http://evolution.genetics.washington.edu/lamarc/index.html Lamarc] main website: Dowload and manual
**[[Lamarc tutorial]]: Demonstration/Tutorial on Monday August 2 ([[Peter Beerli]])
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**[[Lamarc tutorial]]
* MAFFT
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* MIGRATE: Demonstration and Tutorial on July 27  ([[Peter Beerli]])
* MIGRATE: Demonstration/Tutorial on Monday August 1 ([[Peter Beerli]])
 
 
** [http://popgen.sc.fsu.edu Migrate main website]: Download, Manual, Blog/Tutorials, Information on speed, citation of MIGRATE in the literature.
 
** [http://popgen.sc.fsu.edu Migrate main website]: Download, Manual, Blog/Tutorials, Information on speed, citation of MIGRATE in the literature.
** [[Migrate tutorial]]: Tutorial for the course 2011 (same [http://popgen.sc.fsu.edu/Migrate/Tutorials/Entries/2010/7/12_Day_of_longboarding.html] tutorial on the [http://popgen.sc.fsu.edu/Migrate/Tutorials/Tutorials.html Migrate tutorial website])  
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** [[Migrate tutorial 2016]]
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** Tutorial given in 2015  [[Migrate tutorial]]: Tutorial for the course 2014 (an older version can be found here [http://popgen.sc.fsu.edu/Migrate/Tutorials/Entries/2010/7/12_Day_of_longboarding.html tutorial] on the [http://popgen.sc.fsu.edu/Migrate/Tutorials/Tutorials.html Migrate tutorial website])  
 
** [http://groups.google.com/group/migrate-support?lnk=iggc Migrate support google Group]
 
** [http://groups.google.com/group/migrate-support?lnk=iggc Migrate support google Group]
* [http://www.mrbayes.net MrBayes]
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* PAML
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==Similarity searching==
* [http://people.sc.fsu.edu/~dswofford/paup_tesPAUP* PAUP*]
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* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast]
* STEM
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* [http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml Fasta]
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*[http://www.drive5.com/usearch/ USEARCH]

Revision as of 19:25, 20 July 2017

Alignment


Phylogenetic tree building and analysis

Other

Pipelines

Population analysis

Similarity searching