MIGRATE-N

Description

migraten website  

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.

Environment Modules

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

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

System Variables

• HPC_MIGRATEN_DIR - installation directory
• HPC_MIGRATEN_BIN - executable directory
• HPC_MIGRATEN_MAN - manual directory

Additional Information

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

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

Job Script Examples

See the MIGRATE-N_Job_Scripts page for migraten Job script examples.