Difference between revisions of "Software"

From MolEvol
 
(10 intermediate revisions by 5 users not shown)
Line 17: Line 17:
  
 
==Phylogenetic tree building and analysis==
 
==Phylogenetic tree building and analysis==
* [hhttp://beast2.org/ BEAST2] - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
+
* [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]
Line 27: Line 27:
 
**[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.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!)'''
 
**[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!)'''
 +
* [http://www.iqtree.org/ IQ-TREE]
 
* MP-EST
 
* MP-EST
 
** [http://code.google.com/p/mp-est/ Executables, code]
 
** [http://code.google.com/p/mp-est/ Executables, code]
Line 33: Line 34:
 
* [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*]
+
* [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]
Line 48: Line 49:
 
* [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]]
 +
* [http://ipyrad.readthedocs.io/ ipyrad]
  
 
==Pipelines==
 
==Pipelines==
Line 56: Line 58:
 
**[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 25 ([[Peter Beerli]])
+
* MIGRATE: Demonstration and Tutorial on August 8 2019 ([[Peter Beerli]])
** [http://popgen.sc.fsu.edu Migrate main website]: Download, Manual, Blog/Tutorials, Information on speed, citation of MIGRATE in the literature.
+
** [http://peterbeerli.com/migrate-html5/ Migrate main website]: Download, Manual, Blog/Tutorials, Information on speed, citation of MIGRATE in the literature.
** [[Migrate tutorial 2016]]  
+
** [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Migrate tutorial 2018]  
** 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://peterbeerli.com/workshops/mbl/2017/tutorial/ Migrate tutorial 2017], 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]
  
 
==Similarity searching==
 
==Similarity searching==

Latest revision as of 16:40, 21 July 2019

Alignment


Phylogenetic tree building and analysis

Other

Pipelines

Population analysis

Similarity searching