Difference between revisions of "OrthoFinder"

From UFRC
Jump to navigation Jump to search
 
(3 intermediate revisions by 2 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|orthofinder}}
 
|{{#vardefine:app|orthofinder}}
Line 21: Line 21:
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 76: Line 66:
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 17:58, 19 August 2022

Description

orthofinder website  

OrthoFinder is a program for identifying orthologous protein sequence families. It is written in python and runs as a single command that takes as input a directory of FASTA files, one per species. It outputs a file containing the orthologous groups of genes from these species.

Environment Modules

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

System Variables

  • HPC_ORTHOFINDER_DIR - installation directory