IQ-Tree-Teaching - Revision history

Shtsai at 00:52, 5 April 2026

2026-04-05T00:52:16Z

← Older revision		Revision as of 20:52, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]

	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Teaching		Teaching

	=== Version ===		== Version ==

	2.2.2.7, 2.3.5, 2.3.6, 3.0.1		2.2.2.7, 2.3.5, 2.3.6, 3.0.1

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

	Please see http://www.iqtree.org/		Please see http://www.iqtree.org/

	===Description===		==Description==

	Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/		Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/

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

	*Version 2.3.6, installed in /apps/eb/IQ-TREE/2.3.6-gompi-2023a		*Version 2.3.6, installed in /apps/eb/IQ-TREE/2.3.6-gompi-2023a
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	</pre>		</pre>

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

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

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

	[http://www.iqtree.org/ IQ-Tree]		[http://www.iqtree.org/ IQ-Tree]


	=== System ===		== System ==

	64-bit Linux		64-bit Linux

Shtsai: /* Documentation */

2026-01-09T19:49:27Z

Documentation

Show changes

Shtsai: /* Running Program */

2026-01-09T19:48:09Z

Running Program

← Older revision		Revision as of 15:48, 9 January 2026
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	=== Running Program ===		=== Running Program ===

	*Version 2.~~2.2~~.6, installed in /apps/eb/IQ-TREE/2.~~2.2~~.6-gompi-~~2022a~~		*Version 2.3.6, installed in /apps/eb/IQ-TREE/2.3.6-gompi-2023a

	To use this version of IQ-TREE, please first load the module with		To use this version of IQ-TREE, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load IQ-TREE/2.~~2.2~~.6-gompi-~~2022a~~		module load IQ-TREE/2.3.6-gompi-2023a
	</pre>		</pre>
	*Version 1.6.12, installed in /apps/eb/IQ-TREE/1~~.6-12~~-~~foss~~-~~2019b~~		*Version 3.0.1, installed in /apps/eb/IQ-TREE/3.0.1-gompi-2024a

	To use this version of IQ-TREE, please first load the module with		To use this version of IQ-TREE, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load IQ-TREE/1.6.12-~~foss~~-~~2019b~~		module load IQ-TREE/3.0.1-gompi-2024a
	</pre>		</pre>



	Sample job submission script (sub.sh) to run IQ-Tree version. 1.6~~.12~~:		Sample job submission script (sub.sh) to run IQ-Tree version 2.3.6:

	<div class="gscript2">		<div class="gscript2">
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>

	module load IQ-TREE/1.6~~.12~~-~~foss~~-~~2019b~~<br>		module load IQ-TREE/2.3.6-gompi-2023a<br>
	~~iqtree~~ <u>[options]</u><br>		iqtree2 <u>[options]</u><br>
	</div>		</div>

Shtsai: /* Version */

2026-01-09T19:42:12Z

Version

← Older revision		Revision as of 15:42, 9 January 2026
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	=== Version ===		=== Version ===

	1.6.12, 2.2.2.6		2.2.2.7, 2.3.5, 2.3.6, 3.0.1

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

Chelsea: /* Version */

2024-05-09T17:27:09Z

Version

← Older revision		Revision as of 13:27, 9 May 2024
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	=== Version ===		=== Version ===

	1.6.12		1.6.12, 2.2.2.6

	===Author / Distributor===		===Author / Distributor===
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	=== Running Program ===		=== Running Program ===

			*Version 2.2.2.6, installed in /apps/eb/IQ-TREE/2.2.2.6-gompi-2022a

			To use this version of IQ-TREE, please first load the module with
			<pre class="gscript">
			module load IQ-TREE/2.2.2.6-gompi-2022a
			</pre>
	*Version 1.6.12, installed in /apps/eb/IQ-TREE/1.6-12-foss-2019b		*Version 1.6.12, installed in /apps/eb/IQ-TREE/1.6-12-foss-2019b

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	module load IQ-TREE/1.6.12-foss-2019b		module load IQ-TREE/1.6.12-foss-2019b
	</pre>		</pre>

Shtsai at 02:08, 28 August 2020

2020-08-28T02:08:01Z

← Older revision		Revision as of 22:08, 27 August 2020
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	=== Version ===		=== Version ===

	~~1.5.5,~~ 1.6.5		1.6.12

	===Author / Distributor===		===Author / Distributor===
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	=== Running Program ===		=== Running Program ===

	*Version 1.5.5, installed in ~~/usr/local~~/apps/eb/IQ-TREE/1.~~5.5~~-foss-~~2016b-omp-mpi~~		*Version 1.6.12, installed in /apps/eb/IQ-TREE/1.6-12-foss-2019b

	To use this version of IQ-TREE, please first load the module with		To use this version of IQ-TREE, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load IQ-TREE/1.5.5-foss-~~2016b-omp-mpi~~		module load IQ-TREE/1.6.12-foss-2019b
	</pre>		</pre>

	*Version 1.6.5, installed in /usr/local/apps/eb/IQ-TREE/1.6.5-omp

	~~To use this version of IQ-TREE, please first load the module with~~		Sample job submission script (sub.sh) to run IQ-Tree version. 1.6.12:
	~~<pre class="gscript">~~
	~~module load IQ-TREE/1.6.5-omp~~
	~~</pre>~~

	Sample job submission script (sub.sh) to run IQ-Tree version. 1.6.5:

	<div class="gscript2">		<div class="gscript2">
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>

	module load IQ-TREE/1.6.5-~~omp~~<br>		module load IQ-TREE/1.6.12-foss-2019b<br>
	iqtree <u>[options]</u><br>		iqtree <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcomment">		<pre class="gcomment">
	module load IQ-TREE/1.6.5-~~omp~~		module load IQ-TREE/1.6.12-foss-2019b

	iqtree -h		iqtree -h
	IQ-TREE multicore version 1.6.5 for Linux 64-bit built ~~May~~ ~~8 2018~~		IQ-TREE multicore version 1.6.12 for Linux 64-bit built Jul 9 2020
	Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,		Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
	Heiko Schmidt, Dominik Schrempf, Michael Woodhams.		Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
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	-rbal <num_taxa> Create a random balanced tree		-rbal <num_taxa> Create a random balanced tree
	-rcsg <num_taxa> Create a random circular split network		-rcsg <num_taxa> Create a random circular split network
	-rlen <min_len> <mean_len> <max_len>		-rlen <min_len> <mean_len> <max_len>
	min, mean, and max branch lengths of random trees		min, mean, and max branch lengths of random trees

Moses at 16:13, 7 January 2020

2020-01-07T16:13:02Z

← Older revision		Revision as of 12:13, 7 January 2020
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	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
	<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br>		<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br>
	<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br>		<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br>
	<nowiki>#</nowiki>SBATCH --mem=<u>2gb</u><br>		<nowiki>#</nowiki>SBATCH --mem=<u>2gb</u><br>
	<nowiki>#</nowiki>SBATCH --time=<u>04:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>04:00:00</u><br>

Moses at 16:10, 7 January 2020

2020-01-07T16:10:36Z

← Older revision		Revision as of 12:10, 7 January 2020
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	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
	<nowiki>#</nowiki>SBATCH --job-name=u>jobName</u><br>		<nowiki>#</nowiki>SBATCH --job-name=<u>jobName</u><br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>

Moses at 16:10, 7 January 2020

2020-01-07T16:10:21Z

← Older revision		Revision as of 12:10, 7 January 2020
Line 41:		Line 41:
	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
	<nowiki>#</nowiki>SBATCH --job-name=jobName<br>		<nowiki>#</nowiki>SBATCH --job-name=u>jobName</u><br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>

Moses at 16:09, 7 January 2020

2020-01-07T16:09:52Z

← Older revision		Revision as of 12:09, 7 January 2020
Line 41:		Line 41:
	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
	<nowiki>#</nowiki>SBATCH --job-name=~~j_BEDTools~~<br>		<nowiki>#</nowiki>SBATCH --job-name=jobName<br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>