Difference between revisions of "Software"

From MolEvol
(Phylogenetic tree building and analysis)
(Alignment)
 
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==Alignment==
 
==Alignment==
*[http://www.tcoffee.org/ Bali-Phy]
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*[https://ormbunkar.se/aliview/ AliView]
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*[http://faculty.biomath.ucla.edu/msuchard/bali-phy/index.php Bali-Phy]
 
*[ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/ BMGE]
 
*[ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/ BMGE]
 
*[http://fsa.sourceforge.net/ FSA]
 
*[http://fsa.sourceforge.net/ FSA]
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*[http://guidance.tau.ac.il/ Guidance]
 
*[http://guidance.tau.ac.il/ Guidance]
 
*[http://www.jalview.org/ Jalview]
 
*[http://www.jalview.org/ Jalview]
* [http://mafft.cbrc.jp/alignment/software/ MAFFT]
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*[http://mafft.cbrc.jp/alignment/software/ MAFFT]
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*[http://www.megasoftware.net/ MEGA]
 
*[http://www.drive5.com/muscle/ MUSCLE]
 
*[http://www.drive5.com/muscle/ MUSCLE]
 
*[http://opal.cs.arizona.edu/ Opal]
 
*[http://opal.cs.arizona.edu/ Opal]
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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://phylo.bio.ku.edu/content/tracy-heath-dppdiv/ DPPDiv]
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* [http://phylo.bio.ku.edu/content/tracy-heath-dppdiv DPPDiv]
 
*[http://www.microbesonline.org/fasttree/ FastTree]
 
*[http://www.microbesonline.org/fasttree/ FastTree]
* [http://tree.bio.ed.ac.uk/software/figtree/ FigTree]
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* [http://garli.googlecode.com/ Garli]
* GARLI
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**[[Garli_wiki | Documentation wiki ]]
**[http://www.nescent.org/wg_garli/ Support page]
 
**[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!)'''
 +
* [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]
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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]
* [http://www.phylobayes.org/index.html/ PhyloBayes]
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* [http://www.phylobayes.org PhyloBayes]
 
*[http://sco.h-its.org/exelixis/software.html RAxML (and many other programs)]
 
*[http://sco.h-its.org/exelixis/software.html RAxML (and many other programs)]
 +
* [https://revbayes.github.io/download RevBayes]
 
*[http://kiwi.cs.dal.ca/Software/RSPR rSPR]
 
*[http://kiwi.cs.dal.ca/Software/RSPR rSPR]
 
*[http://kiwi.cs.dal.ca/Software/SPRSupertrees SPRSupertrees]
 
*[http://kiwi.cs.dal.ca/Software/SPRSupertrees SPRSupertrees]
 
* [http://www.stat.osu.edu/~lkubatko/software/STEM/ STEM]
 
* [http://www.stat.osu.edu/~lkubatko/software/STEM/ STEM]
* [http://tree.bio.ed.ac.uk/software/tracer/ Tracer]
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* [https://github.com/beast-dev/tracer/releases/tag/v1.7.1 Tracer]
 
*[http://evolution.gs.washington.edu/phylip/software.html Comprehensive list of Phylogeny programs]
 
*[http://evolution.gs.washington.edu/phylip/software.html Comprehensive list of Phylogeny programs]
 +
 +
==Post-Hoc Tree Analysis or manipulation==
 +
* [http://pythonhosted.org/DendroPy/ DendroPy] (Fantastic for summarizing posteriors, distance calculations, and simulation)
 +
* [http://cegg.unige.ch/newick_utils Newick Utilities] (Rerooting and tree parsing from the command line)
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 +
==Tree Viewing and Plotting==
 +
* [https://github.com/rambaut/figtree/releases FigTree]
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* [https://github.com/GuangchuangYu/ggtree ggTree] (R package for producing publication-quality trees with metadata)
  
 
==Other==
 
==Other==
 
* [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]]
  
 
==Pipelines==
 
==Pipelines==
*[https://bitbucket.org/caseywdunn/agalma Agalma]
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*[https://bitbucket.org/caseywdunn/agalma Agalma] (Transcriptome assembly and analysis)
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* [http://ipyrad.readthedocs.io/ ipyrad] (RADseq data assembly and analysis)
  
 
==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 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.
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** [http://peterbeerli.com/migrate-html5/ 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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** [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Migrate tutorial 2018]
** [http://groups.google.com/group/migrate-support?lnk=iggc Migrate support google Group]
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** [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]
  
 
==Similarity searching==
 
==Similarity searching==

Latest revision as of 18:09, 3 August 2019

Alignment

Phylogenetic tree building and analysis

Post-Hoc Tree Analysis or manipulation

  • DendroPy (Fantastic for summarizing posteriors, distance calculations, and simulation)
  • Newick Utilities (Rerooting and tree parsing from the command line)

Tree Viewing and Plotting

  • FigTree
  • ggTree (R package for producing publication-quality trees with metadata)

Other

Pipelines

  • Agalma (Transcriptome assembly and analysis)
  • ipyrad (RADseq data assembly and analysis)

Population analysis

Similarity searching