OrthoFinder-Sapelo2 - Revision history

Shtsai at 01:16, 5 April 2026

2026-04-05T01:16:37Z

← Older revision		Revision as of 21:16, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	2.5.4, 2.5.5		2.5.4, 2.5.5

	=== Author / Distributor ===		== Author / Distributor ==

	[https://github.com/davidemms/OrthoFinder OrthoFinder]		[https://github.com/davidemms/OrthoFinder OrthoFinder]

	=== Description ===		== Description ==
	"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format."		"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format."
	More details are at [https://github.com/davidemms/OrthoFinder OrthoFinder]		More details are at [https://github.com/davidemms/OrthoFinder OrthoFinder]

	=== Running Program ===		== Running Program ==

	Please refer to [[Running Jobs on Sapelo2]]		Please refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	source code from [https://github.com/davidemms/OrthoFinder/releases OrthoFinder]		source code from [https://github.com/davidemms/OrthoFinder/releases OrthoFinder]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Jordan: Updated to reflect that necessary (default) tools are included in OrthoFinder/2.5.5-foss-2022a. Will update further when OrthoFinder/2.5.5-foss-2023a has been fixed.

2024-06-24T16:24:16Z

Updated to reflect that necessary (default) tools are included in OrthoFinder/2.5.5-foss-2022a. Will update further when OrthoFinder/2.5.5-foss-2023a has been fixed.

← Older revision		Revision as of 12:24, 24 June 2024
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	Please refer to [[Running Jobs on Sapelo2]]		Please refer to [[Running Jobs on Sapelo2]]

	*Version 2.5.4, installed at /apps/eb/OrthoFinder/2.5.4-foss-2022a/

	To use ~~the~~ version 2.5.4, please first load the module with		'''Version 2.5.4'''

			Version 2.5.4, installed at
			*/apps/eb/OrthoFinder/2.5.4-foss-2022a/

			To use version 2.5.4, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	ml OrthoFinder/2.5.4-foss-2022a		ml OrthoFinder/2.5.4-foss-2022a
	</pre>		</pre>
			</br>
			'''Version 2.5.5'''

			Version 2.5.5, installed at
			*/apps/eb/OrthoFinder/2.5.5-foss-2022a/

			To use version 2.5.5, please first load the module with

	Here is an example of a shell script sub.sh to run ~~orthofinder of version 2~~.5.4 at the batch queue:		<pre class="gscript">
			ml OrthoFinder/2.5.5-foss-2022a
			</pre>
			</br>
			Note that if the option<pre class="gscript">-M msa</pre>is used as shown in the documentation below, this will allow for both multiple sequence alignment building as well as tree inference. The default methods for these processes (MAFFT and FastTree, respectively) are loaded with OrthoFinder/2.5.5-foss-2022a, but if you wish to use alternative methods as described in the documentation, you will need to load the modules for these methods yourself. Please refer to [[Available Toolchains and Toolchain Compatibility]] if you are unsure of what installations of these software will be compatible with our installation of OrthoFinder.

			Here is an example of a shell script sub.sh to run OrthoFinder v2.5.5 at the batch queue:
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml OrthoFinder/2.5.4-foss-2022a		ml OrthoFinder/2.5.5-foss-2022a

	orthofinder -t 8 -a 8 [options]		orthofinder -t 8 -a 8 [options]
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	<pre class="gcommand">		<pre class="gcommand">
	ml OrthoFinder/2.5.4-foss-2022a		ml OrthoFinder/2.5.5-foss-2022a
	orthofinder -h		orthofinder -h

	OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms		OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

	SIMPLE USAGE:		SIMPLE USAGE:
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	-s <file> User-specified rooted species tree		-s <file> User-specified rooted species tree
	-I <int> MCL inflation parameter [Default = 1.5]		-I <int> MCL inflation parameter [Default = 1.5]
			--fewer-files Only create one orthologs file per species
	-x <file> Info for outputting results in OrthoXML format		-x <file> Info for outputting results in OrthoXML format
	-p <dir> Write the temporary pickle files to <dir>		-p <dir> Write the temporary pickle files to <dir>

Chelsea: /* Version */

2024-05-13T20:46:05Z

Version

← Older revision		Revision as of 16:46, 13 May 2024
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	=== Version ===		=== Version ===
	2.5.4		2.5.4, 2.5.5

	=== Author / Distributor ===		=== Author / Distributor ===

Moses at 15:46, 5 September 2023

2023-09-05T15:46:50Z

← Older revision		Revision as of 11:46, 5 September 2023
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	=== Version ===		=== Version ===
	~~2.3.8, 2.3.11,~~ 2.5.2		2.5.4

	=== Author / Distributor ===		=== Author / Distributor ===
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	Please refer to [[Running Jobs on Sapelo2]]		Please refer to [[Running Jobs on Sapelo2]]

	*Version 2.~~3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16~~		*Version 2.5.4, installed at /apps/eb/OrthoFinder/2.5.4-foss-2022a/
	*Version 2.3.11, installed at /apps/eb/OrthoFinder/2.3.11-intel-2019b-Python-3.7.4
	*Version 2.5.2, installed at /apps/eb/OrthoFinder/2.5.2-foss-~~2019b-Python-3.7.4~~

			To use the version 2.5.4, please first load the module with
	To use the version 2.3.~~8, please first load the module with~~

	~~<pre class="gscript">~~
	~~ml OrthoFinder/2.3.8-foss-2019b-Python-2.7.16~~
	~~</pre>~~

	~~To use the version 2.3.1~~, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	ml OrthoFinder/2.3.~~11-intel-2019b~~-~~Python~~-~~3.7.4~~		ml OrthoFinder/2.5.4-foss-2022a
	</pre>		</pre>

	~~To use the version 2.5.2, please first load the module with~~

	~~<pre class="gscript">~~		Here is an example of a shell script sub.sh to run orthofinder of version 2.5.4 at the batch queue:
	~~ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4~~
	~~</pre>~~


	Here is an example of a shell script sub.sh to run orthofinder~~.py~~ of version 2.5.2 at the batch queue:
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml OrthoFinder/2.5.2-foss-~~2019b-Python-3.7.4~~		ml OrthoFinder/2.5.4-foss-2022a

	orthofinder -t 8 -a 8 [options]		orthofinder -t 8 -a 8 [options]
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	=== Documentation ===		=== Documentation ===

	<pre class="gcommand">		<pre class="gcommand">
	ml OrthoFinder/2.5.2-foss-~~2019b-Python-3.7.4~~		ml OrthoFinder/2.5.4-foss-2022a
	orthofinder -h		orthofinder -h

	OrthoFinder version 2.5.2 Copyright (C) 2014 David Emms		OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

	SIMPLE USAGE:		SIMPLE USAGE:
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	OPTIONS:		OPTIONS:
	-t <int> Number of parallel sequence search threads [Default = 64]		-t <int> Number of parallel sequence search threads [Default = 16]
	-a <int> Number of parallel analysis threads		-a <int> Number of parallel analysis threads
	-d Input is DNA sequences		-d Input is DNA sequences

Moses at 15:50, 20 May 2021

2021-05-20T15:50:54Z

← Older revision		Revision as of 11:50, 20 May 2021
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	ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4		ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4

	orthofinder~~.py~~ -t 8 -a 8 [options]		orthofinder -t 8 -a 8 [options]
	</pre>		</pre>

Moses at 15:19, 20 May 2021

2021-05-20T15:19:13Z

← Older revision		Revision as of 11:19, 20 May 2021
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	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
	#SBATCH --cpus-per-task=2		#SBATCH --cpus-per-task=8
	#SBATCH --mem=~~10gb~~		#SBATCH --mem=32gb
	#SBATCH --time=120:00:00		#SBATCH --time=120:00:00
	#SBATCH --output=log.%j.out		#SBATCH --output=log.%j.out
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	ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4		ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4

	orthofinder.py [options]		orthofinder.py -t 8 -a 8 [options]
	</pre>		</pre>

Moses: /* Documentation */

2021-05-20T15:13:59Z

Documentation

← Older revision		Revision as of 11:13, 20 May 2021
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	<pre class="gcommand">		<pre class="gcommand">
	ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4		ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4
	~~zhuofei@b1-24 ~$~~ orthofinder -h		orthofinder -h

	OrthoFinder version 2.5.2 Copyright (C) 2014 David Emms		OrthoFinder version 2.5.2 Copyright (C) 2014 David Emms

Moses: /* Running Program */

2021-05-20T15:11:42Z

Running Program

← Older revision		Revision as of 11:11, 20 May 2021
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	=== Running Program ===		=== Running Program ===

	~~Also~~ refer to [[Running Jobs on Sapelo2]]		Please refer to [[Running Jobs on Sapelo2]]

	*Version 2.3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16		*Version 2.3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16

Moses: /* Running Program */

2021-05-20T15:10:45Z

Running Program

← Older revision		Revision as of 11:10, 20 May 2021
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
	~~Also refer to [[Running_Jobs_on_Sapelo2#Running_an_X-windows_application \| Run X window Jobs]] and~~
	~~[[Running_Jobs_on_Sapelo2#Running_an_Interactive_Job \| Run interactive Jobs]]~~

	*Version 2.3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16		*Version 2.3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16
	*Version 2.3.11, installed at /apps/eb/OrthoFinder/2.3.11-intel-2019b-Python-3.7.4		*Version 2.3.11, installed at /apps/eb/OrthoFinder/2.3.11-intel-2019b-Python-3.7.4
	*Version 2.5.2, installed at /apps/eb/OrthoFinder/2.5.2-foss-2019b-Python-3.7.4		*Version 2.5.2, installed at /apps/eb/OrthoFinder/2.5.2-foss-2019b-Python-3.7.4


	To use the version 2.3.8, please first load the module with		To use the version 2.3.8, please first load the module with

Moses at 15:10, 20 May 2021

2021-05-20T15:10:14Z

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