Difference between revisions of "MIGRATE-N"
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| − | [[Category:Software | + | __NOTOC__ |
| − | {|<!-- | + | __NOEDITSECTION__ |
| + | [[Category:Software]] | ||
| + | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|migraten}} | |{{#vardefine:app|migraten}} | ||
|{{#vardefine:url|http://popgen.sc.fsu.edu/Migrate/Migrate-n.html}} | |{{#vardefine:url|http://popgen.sc.fsu.edu/Migrate/Migrate-n.html}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> |
| − | |{{#vardefine: | + | |{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link--> |
| − | + | |{{#vardefine:policy|}} <!--Enable policy section --> | |
| − | |{{#vardefine: | + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> |
| − | |{{#vardefine: | + | |{{#vardefine:faq|}} <!--Enable FAQ section --> |
| − | |{{#vardefine: | + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> |
| − | |{{#vardefine: | ||
| − | |{{#vardefine: | ||
|} | |} | ||
| − | <!-- | + | <!-- ######## Template Body ######## --> |
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | 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. | + | 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. | ||
<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | ==Environment Modules== | ||
| − | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | + | Run <code>$ module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| + | |||
| + | ===Serial Module=== | ||
| + | For the serial binary: | ||
| + | |||
| + | <code>$ module load migraten/4.4.4</code> | ||
| + | |||
| + | ===Parallel Module (MPI)=== | ||
| + | For the MPI binary: | ||
| + | |||
| + | <code>$ module load intel/2020 openmpi/4.0.4 migraten/4.4.4</code> | ||
| + | |||
| + | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| − | * | + | * HPC_MIGRATEN_BIN - executable directory |
* HPC_{{uc:{{#var:app}}}}_MAN - manual directory | * HPC_{{uc:{{#var:app}}}}_MAN - manual directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | A manual page is available. Run '''man migrate''' to view it after loading the appropriate module. | ||
| − | + | Full manual is available from the [http://popgen.sc.fsu.edu/migratedoc.pdf Migrate-n website]. | |
| − | |||
| − | |||
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| − | + | Serial command example: | |
| + | migrate-n parmfile -nomenu | ||
| + | Parallel command example: | ||
| + | mpiexec migrate-n-mpi parmfile -nomenu | ||
|}} | |}} | ||
| − | + | ||
| − | {{#if: {{#var: | + | {{#if: {{#var: conf}}|==Configuration== |
| − | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples. | + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} |
| − | |}} | + | {{#if: {{#var: pbs}}|==Job Script Examples== |
| − | + | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.|}} | |
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | |
| − | WRITE USAGE POLICY HERE ( | ||
| − | |||
| − | |}} | ||
| − | |||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | |
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| − | |}} | ||
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{{#if: {{#var: faq}}|==FAQ== | {{#if: {{#var: faq}}|==FAQ== | ||
*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
| − | |||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{ | + | If you publish research that uses {{{app}}} you have to cite it as follows: |
| − | + | WRITE CITATION HERE | |
| − | |||
| − | |||
|}} | |}} | ||
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Revision as of 18:02, 27 May 2022
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.
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/4.0.4 migraten/4.4.4
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:
mpiexec migrate-n-mpi parmfile -nomenu
Job Script Examples
See the MIGRATE-N_Job_Scripts page for migraten Job script examples.