Tag: Migration Rate

IMIG – Infer Recent Migration rates from Individual Genotypes

IMIG

:: DESCRIPTION

IMIG (Inferring recent Migration rates from Individual Genotypes) aims at estimating pairwise rates of migration between discrete populations using multilocus genotypes.

::DEVELOPER

Thomas Broquet (thomas.broquet@unil.ch) and Jon Yearsley (jon.yearsley@ucd.ie)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 IMIG

:: MORE INFORMATION

Citation

Mol Ecol. 2009 Mar;18(6):1048-60. Epub 2009 Feb 9.
Inferring recent migration rates from individual genotypes.
Broquet T, Yearsley J, Hirzel AH, Goudet J, Perrin N.

Migrate 4.4.3 – Estimate Population Sizes & Migration Rates

Migrate 4.4.3

:: DESCRIPTION

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.

It can use the following data types:

  • Sequence data using Felsenstein’s 84 model with or without site rate variation,
  • Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)
  • Microsatellite data using a stepwise mutation model or a brownian motion mutation model (using the repeatlength input format or the fragment-length input format),
  • Electrophoretic data using an ‘infinite’ allele model.

::DEVELOPER

Peter Beerli

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix

:: DOWNLOAD

Migrate-N

:: MORE INFORMATION

Citation

Population Genetic Inference With MIGRATE.
Beerli P, Mashayekhi S, Sadeghi M, Khodaei M, Shaw K.
Curr Protoc Bioinformatics. 2019 Dec;68(1):e87. doi: 10.1002/cpbi.87.

PMLE 2.0 – Maximum Likelihood Estimation of Migration Rates for Wright Island Model

PMLE 2.0

:: DESCRIPTION

PMLE estimates the gene flow parameter q for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either single or multi locus, haploid or diploid, genotype data. Suitable molecular data types minimally include allozymes, microsatellites, and RFLPs.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 PMLE

:: MORE INFORMATION

Citation

Rannala, B., and J. A. Hartigan. 1996.
Estimating gene flow in island populations.
Genetical Research 67:147-158

MDIV – Estimate Divergence Times and Migration Rates between two Populations

MDIV

:: DESCRIPTION

MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MDIV

:: MORE INFORMATION

Citation:

Genetics. 2001 Jun;158(2):885-96.
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
Nielsen R, Wakeley J.