Difference between revisions of "ExposedPrograms"

 
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The program Structure ([http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/html/structure.html download website] uses genotpyic data to assign individuals to populations probabilistically.
 
The program Structure ([http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/html/structure.html download website] uses genotpyic data to assign individuals to populations probabilistically.
  
'''[[StructureTheory | Theory]] [[StructureTutorial | Tutorial]]'''
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'''[[StructureTheory | Theory]] [[StructureTutorial | Tutorial]] [[StructureReport | Example Report]]'''
  
 
=== Dadi ===
 
=== Dadi ===
 
The program dadi ([https://bitbucket.org/RyanGutenkunst/dadi download website] uses the site frequency spectrum to evaluate complex population models, up to three populations.
 
The program dadi ([https://bitbucket.org/RyanGutenkunst/dadi download website] uses the site frequency spectrum to evaluate complex population models, up to three populations.
  
'''[[DadiTheory | Theory]] [[DadiTutorial | Tutorial]]'''
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'''[[DadiTheory | Theory]] [[DadiTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
  
 
=== Treemix ===
 
=== Treemix ===
 
The program treemix [https://bitbucket.org/nygcresearch/treemix/wiki/Home download website]
 
The program treemix [https://bitbucket.org/nygcresearch/treemix/wiki/Home download website]
  
'''[[TreemixTheory | Theory]] [[TreemixTutorial | Tutorial]]'''
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'''[[TreemixTheory | Theory]] [[TreemixTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
  
 
=== Geneland ===
 
=== Geneland ===
 
The program Geneland (it is an R package an can be installed from any CRAN site - see instructions)
 
The program Geneland (it is an R package an can be installed from any CRAN site - see instructions)
  
'''[[GenelandTheory | Theory]] [[GenelandTutorial | Tutorial]]'''
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'''[[GenelandTheory | Theory]] [[GenelandTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
  
 
=== Sate ===
 
=== Sate ===
 
The program Sate estimates a phylogenetic tree and aligns sequences at the same time.
 
The program Sate estimates a phylogenetic tree and aligns sequences at the same time.
  
'''[[SateTheory | Theory]] [[SateTutorial | Tutorial]]'''
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'''[[SateTheory | Theory]] [[SateTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
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 +
 
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=== RevBayes ===
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RevBayes is a very versatile Bayesian inference system geared towards phylogenetic analysis. It has an R-like interface with its own language Rev.
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'''[[RevBayesTheory | Theory]] [[RevBayesTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
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=== BEAST 1.8 Skyline ===
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Beast is a versatile package to analyze phylogenies population expansion and plots of parameters through time.
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'''[[BeastTheory | Theory]] [[BeastSkyTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
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=== BEAST 2.3 SNAPP ===
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SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP).
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'''[[BeastSNAPPTheory | Theory]] [[BeastSNAPPTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
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=== IMa ===
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IMa  estimates divergence times and population sizes and migration rates among populations using sequence data.
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'''[[IMaTheory | Theory]] [[IMaTutorial | Tutorial]]  [[StructureReport | Example Report]]'''
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=== Migrate ===
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Migrate  estimates population sizes, migration rates, and (in a very recent version) divergence times and  among populations using sequence or microsatellite data.
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'''[[MigrateTheory | Theory]] [[MigrateCLASSTutorial | Tutorial]] [[MigrateTutorial | MBL-Tutorial]]  [[StructureReport | Example Report]]'''

Latest revision as of 07:47, 18 November 2015

Description of programs and tutorials

Here, you can find the programs we discussed, having a short summary about the programs and their inner working and a short tutorial of the program.

Genepop

Genepop on the Web and Genepop Software This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc.

Theory; Tutorial material: download GENEPOP_TUTORIAL.ZIP

Structure

The program Structure (download website uses genotpyic data to assign individuals to populations probabilistically.

Theory Tutorial Example Report

Dadi

The program dadi (download website uses the site frequency spectrum to evaluate complex population models, up to three populations.

Theory Tutorial Example Report

Treemix

The program treemix download website

Theory Tutorial Example Report

Geneland

The program Geneland (it is an R package an can be installed from any CRAN site - see instructions)

Theory Tutorial Example Report

Sate

The program Sate estimates a phylogenetic tree and aligns sequences at the same time.

Theory Tutorial Example Report


RevBayes

RevBayes is a very versatile Bayesian inference system geared towards phylogenetic analysis. It has an R-like interface with its own language Rev.

Theory Tutorial Example Report


BEAST 1.8 Skyline

Beast is a versatile package to analyze phylogenies population expansion and plots of parameters through time.

Theory Tutorial Example Report


BEAST 2.3 SNAPP

SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP).

Theory Tutorial Example Report

IMa

IMa estimates divergence times and population sizes and migration rates among populations using sequence data.

Theory Tutorial Example Report

Migrate

Migrate estimates population sizes, migration rates, and (in a very recent version) divergence times and among populations using sequence or microsatellite data.

Theory Tutorial MBL-Tutorial Example Report