Difference between revisions of "Software"

From MolEvol
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*[http://pbil.univ-lyon1.fr/software/seaview.html SeaView]
 
*[http://pbil.univ-lyon1.fr/software/seaview.html SeaView]
 
*[http://www.tcoffee.org/ T-Coffee]
 
*[http://www.tcoffee.org/ T-Coffee]
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==Phylogenetic tree building and analysis==
 
==Phylogenetic tree building and analysis==
* [http://beast.bio.ed.ac.uk/Main_Page BEAST] - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
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* [http://www.beast2.org/ BEAST2] - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
 
* [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST]
 
* [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST]
 
* [http://pythonhosted.org/DendroPy/ DendroPy]
 
* [http://pythonhosted.org/DendroPy/ DendroPy]
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*[http://www.microbesonline.org/fasttree/ FastTree]
 
*[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]
 
 
**[http://groups.google.com/group/garli_users/ Google users group]
 
**[http://groups.google.com/group/garli_users/ Google users group]
**[http://phylo.bio.ku.edu/slides/GarliDemo/garliExercise.html Workshop tutorial] '''(NOTE: The tutorial bundle linked on this page contains everything you need - you don't need to download the program separately!)'''
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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!)'''
 
* MP-EST
 
* MP-EST
 
** [http://code.google.com/p/mp-est/ Executables, code]
 
** [http://code.google.com/p/mp-est/ Executables, code]
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* [http://statgen.ncsu.edu/thorne/multidivtime.html multidivtime]
 
* [http://statgen.ncsu.edu/thorne/multidivtime.html multidivtime]
 
* [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
 
* [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
* [http://people.sc.fsu.edu/~dswofford/paup_test PAUP*]
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* [http://phylosolutions.com/paup-test PAUP*]
 
* [http://code.google.com/p/phybase/ PHYBASE]
 
* [http://code.google.com/p/phybase/ PHYBASE]
 
* [http://pbil.univ-lyon1.fr/software/phyldog/ PHYLDOG]
 
* [http://pbil.univ-lyon1.fr/software/phyldog/ PHYLDOG]
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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).
 
* [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).
 
*[[Media:MCMCEG.zip | MCMC example software]] from [[John_Huelsenbeck | John Huelsenbeck]]
 
*[[Media:MCMCEG.zip | MCMC example software]] from [[John_Huelsenbeck | John Huelsenbeck]]
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* [http://ipyrad.readthedocs.io/ ipyrad]
  
 
==Pipelines==
 
==Pipelines==
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==Population analysis==
 
==Population analysis==
* LAMARC: Demonstration and Tutorial on July 29 ([[Peter Beerli]])
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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]]
 
**[[Lamarc tutorial]]
* MIGRATE: Demonstration and Tutorial on July 29 ([[Peter Beerli]])
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* MIGRATE: Demonstration and Tutorial on July 27  ([[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 2012 (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]
  

Revision as of 19:25, 20 July 2017

Alignment


Phylogenetic tree building and analysis

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