Tag: Population Size

IBDNe 20200423 – Estimate Effective Population size in recent Generations

IBDNe 20200423

:: DESCRIPTION

The IBDNe program estimate ancestry-specific historical effective population size.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

IBDNe

:: MORE INFORMATION

Citation:

Browning SR, Browning BL.
Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.
Am J Hum Genet. 2015 Sep 3;97(3):404-18. doi: 10.1016/j.ajhg.2015.07.012. Epub 2015 Aug 20. PMID: 26299365; PMCID: PMC4564943.

VarEff 1.2 – Detecting the Evolution of the Coalescent Effective Population Size

VarEff 1.2

:: DESCRIPTION

VarEff estimates the effective sizes from actual to ancestral time with a coalescent approach. It works on steps of constant size to resolve the probabilities by an approximation of maximum likelihood from a Bayesian posterior distribution.

::DEVELOPER

VarEff Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R pacakge

:: DOWNLOAD

 VarEff

:: MORE INFORMATION

Citation

Chevalet C & Nikolic N. 2010.
Distribution of coalescent times and distances between microsatellite alleles with changing effective population size.
Theoretical Population Biology. Volume 77, Issue 3: 152-163

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.