Difference between revisions of "Ibdne"

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m (Reverted edits by Israel.herrera (talk) to last revision by Moskalenko)
Tag: Rollback
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
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|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
The IBDNe program estimates the historical effective population size of a homogenous population. The input for the IBDNe program is the set of identity-by-descent (IBD) segments detected by the IBDseq program.
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The IBDNe program estimates the historical effective population size of a homogenous population. The input for the IBDNe program is the set of identity-by-descent (IBD) segments detected by the IBDseq program.  
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
IBDseq is part of IBDNe.
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
  
 
|}}
 
|}}
<!--PBS scripts-->
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<!--Job Scripts-->
{{#if: {{#var: pbs}}|==PBS Script Examples==
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{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
 
|}}
 
|}}
 
<!--Policy-->
 
<!--Policy-->
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
  
[http://www.cell.com/ajhg/abstract/S0002-9297(15)00288-8 S R Browning and B L Browning (2015) Accurate non-parametric estimation of recent effective population size from segments of identity by descent. American Journal of Human Genetics. In Press. doi:10.1016/j.ajhg.2015.07.012]
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S R Browning and B L Browning (2015). Accurate non-parametric estimation of recent effective population size from segments of identity by descent. American Journal of Human Genetics 97(3):404-418. doi:10.1016/j.ajhg.2015.07.012
  
 
|}}
 
|}}

Revision as of 17:03, 27 May 2022

Description

ibdne website  

The IBDNe program estimates the historical effective population size of a homogenous population. The input for the IBDNe program is the set of identity-by-descent (IBD) segments detected by the IBDseq program.

Environment Modules

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

System Variables

  • HPC_IBDNE_DIR - installation directory
  • HPC_IBDNE_BIN - executable directory




Citation

If you publish research that uses ibdne you have to cite it as follows:

S R Browning and B L Browning (2015). Accurate non-parametric estimation of recent effective population size from segments of identity by descent. American Journal of Human Genetics 97(3):404-418. doi:10.1016/j.ajhg.2015.07.012