Difference between revisions of "ExposedPrograms"
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=== Genepop === | === Genepop === | ||
[http://genepop.curtin.edu.au Genepop on the Web] and [http://kimura.univ-montp2.fr/~rousset/Genepop.htm Genepop Software] This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc. | [http://genepop.curtin.edu.au Genepop on the Web] and [http://kimura.univ-montp2.fr/~rousset/Genepop.htm Genepop Software] This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc. | ||
| − | + | ||
| − | + | ''' [[genepop_background | Theory]]; | |
| − | + | Tutorial material: download [http://peterbeerli.com/classdata/ISC5935ppg/genepop_tutorial.zip GENEPOP_TUTORIAL.ZIP]''' | |
| − | + | ||
| − | ''' [[ | + | === Structure === |
| − | '''Tutorial | + | 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]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | === 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. | ||
| + | |||
| + | '''[[DadiTheory | Theory]] [[DadiTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | === Treemix === | ||
| + | The program treemix [https://bitbucket.org/nygcresearch/treemix/wiki/Home download website] | ||
| + | |||
| + | '''[[TreemixTheory | Theory]] [[TreemixTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | === Geneland === | ||
| + | The program Geneland (it is an R package an can be installed from any CRAN site - see instructions) | ||
| + | |||
| + | '''[[GenelandTheory | Theory]] [[GenelandTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | === Sate === | ||
| + | The program Sate estimates a phylogenetic tree and aligns sequences at the same time. | ||
| + | |||
| + | '''[[SateTheory | Theory]] [[SateTutorial | Tutorial]] [[StructureReport | 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. | ||
| + | |||
| + | '''[[RevBayesTheory | Theory]] [[RevBayesTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | |||
| + | === BEAST 1.8 Skyline === | ||
| + | Beast is a versatile package to analyze phylogenies population expansion and plots of parameters through time. | ||
| + | |||
| + | '''[[BeastTheory | Theory]] [[BeastSkyTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | |||
| + | === BEAST 2.3 SNAPP === | ||
| + | SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP). | ||
| + | |||
| + | '''[[BeastSNAPPTheory | Theory]] [[BeastSNAPPTutorial | Tutorial]] [[StructureReport | Example Report]]''' | ||
| + | |||
| + | === IMa === | ||
| + | IMa estimates divergence times and population sizes and migration rates among populations using sequence data. | ||
| + | |||
| + | '''[[IMaTheory | Theory]] [[IMaTutorial | Tutorial]] [[StructureReport | 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. | ||
| + | |||
| + | '''[[MigrateTheory | Theory]] [[MigrateCLASSTutorial | Tutorial]] [[MigrateTutorial | MBL-Tutorial]] [[StructureReport | Example Report]]''' | ||
Latest revision as of 06:47, 18 November 2015
Contents
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.
