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MIGRATE-N

Description

migraten website

Migrate-n 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.

This module provides the serial and the threaded versions of Migrate-N. Load the migraten/3.6.6-mpi module to access the MPI version or add the "intel" and "openmpi" modules and then load migraten/3.6.6.

Environment Modules

Run module spider migraten to find out what environment modules are available for this application.

Environment Variables

  • HPC_MIGRATEN_DIR - installation directory
  • HPC_MIGRATEN_BIN - executable directory

Additional Usage Information

Loading the Module:

Serial Module:

For the serial binary 

$ module load migraten/4.4.4

Parallel Module (MPI):

For the MPI binary 

$ module load intel/2020 openmpi/4.1.1 migraten/5.0.4

Additional Help:

A manual page is available. Run man migrate to view it after loading the appropriate module.

A full manual is available from the Migrate-n Website.

Serial command example: 

$ migrate-n parmfile -nomenu

Parallel command example: 

$ migrate-n OR $ mpiexec migrate-n-mpi parmfile -nomenu

Categories

biology, genomics