PAML-Teaching - Revision history

Shtsai at 01:17, 5 April 2026

2026-04-05T01:17:24Z

← Older revision		Revision as of 21:17, 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 ==
	4.9j, 4.10.5		4.9j, 4.10.5

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

	[http://abacus.gene.ucl.ac.uk/software/paml.html PAML]		[http://abacus.gene.ucl.ac.uk/software/paml.html PAML]

	=== Description ===		== Description ==
	"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."		"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."
	More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]		More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]

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

	Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCCcore-11.3.0		Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCCcore-11.3.0
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	</pre>		</pre>

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

	Please see http://abacus.gene.ucl.ac.uk/software/paml.html		Please see http://abacus.gene.ucl.ac.uk/software/paml.html
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	Source code is obtained from [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]		Source code is obtained from [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]

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

Shtsai at 19:57, 9 January 2026

2026-01-09T19:57:17Z

← Older revision		Revision as of 15:57, 9 January 2026
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	=== Running Program ===		=== Running Program ===

	Version 4.9j of this application is at /apps/eb/PAML/4.9j-~~GCC~~-11.2.0		Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCCcore-11.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml PAML/4.9j-~~GCC~~-11.2.0		ml PAML/4.9j-GCCcore-11.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml PAML/4.9j-~~GCC~~-11.2.0<br>		ml PAML/4.9j-GCCcore-11.3.0<br>
	baseml <u>[options]</u><br>		baseml <u>[options]</u><br>
	</div>		</div>

Chelsea: /* Version */

2024-05-13T20:47:16Z

Version

← Older revision		Revision as of 16:47, 13 May 2024
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	=== Version ===		=== Version ===
	4.9j		4.9j, 4.10.5

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

Shtsai at 18:04, 6 September 2023

2023-09-06T18:04:47Z

← Older revision		Revision as of 14:04, 6 September 2023
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	=== Version ===		=== Version ===
	4.9i		4.9j

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

	Version 4.9i of this application is at /apps/eb/PAML/4.9i-GCC-8.3.0		Version 4.9j of this application is at /apps/eb/PAML/4.9j-GCC-11.2.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml PAML/4.9i-GCC-8.3.0		ml PAML/4.9j-GCC-11.2.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml PAML/4.9i-GCC-8.3.0<br>		ml PAML/4.9j-GCC-11.2.0<br>
	baseml <u>[options]</u><br>		baseml <u>[options]</u><br>
	</div>		</div>

Shtsai at 02:18, 28 August 2020

2020-08-28T02:18:13Z

← Older revision		Revision as of 22:18, 27 August 2020
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	=== Version ===		=== Version ===
	4.9h		4.9i

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

	~~The last version~~ of this application is at ~~/usr/local~~/apps/eb/PAML/4.9h-~~foss~~-~~2016b~~		Version 4.9i of this application is at /apps/eb/PAML/4.9i-GCC-8.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml PAML/4.9h-~~foss~~-~~2016b~~		ml PAML/4.9i-GCC-8.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml PAML/4.9h-~~foss~~-~~2016b~~<br>		ml PAML/4.9i-GCC-8.3.0<br>
	~~which~~ baseml <u>[options]</u><br>		baseml <u>[options]</u><br>
	</div>		</div>
	In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.		In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
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	=== Documentation ===		=== Documentation ===

	~~<pre class="gcommand">~~		Please see http://abacus.gene.ucl.ac.uk/software/paml.html
	~~ml PAML~~/4.~~9h-foss-2016b~~
	~~which baseml~~
	~~/usr/local~~/~~apps~~/~~eb/PAML/4~~.~~9h-foss-2016b/bin/baseml~~

	~~</pre>~~
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Yhuang at 16:21, 15 August 2018

2018-08-15T16:21:57Z

← Older revision		Revision as of 12:21, 15 August 2018
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	=== Description ===		=== Description ===
	"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."		"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."
			More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
	~~A summary of the types of analyses performed by different programs:~~

	~~'''baseml''': ML analysis of nucleotide sequences~~

	~~'''basemlg''': ML analysis of nucleotide sequences under the model of gamma rates among sites.~~

	~~'''codonml''' (codeml with seqtype = 1): ML analysis of protein-coding DNA sequences~~

	~~'''aaml''' (codeml with seqtype = 2): ML analysis of amino acid sequences under a number of amino acid substitution models~~

	~~'''pamp''': Parsimony-based analyses for a given tree topology~~

	~~'''mcmctree''': Bayesian estimation of phylogenies using DNA sequence data~~

	~~'''evolver''': This program used to be named listtree~~

	~~'''yn00:''' estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.~~

	~~Please refer to~~ [http://abacus.gene.ucl.ac.uk/software/paml.html~~#introduction~~ PAML] ~~for more details.~~

	=== Running Program ===		=== Running Program ===
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	<pre class="gcommand">		<pre class="gcommand">
	ml PAML/4.9h-foss-2016b		ml PAML/4.9h-foss-2016b
	cd /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin		which baseml
	ls		/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml
	baseml ~~basemlg chi2 codeml evolver pamp yn00~~

	</pre>		</pre>

Yhuang at 19:32, 10 August 2018

2018-08-10T19:32:40Z

@@ Line 17: / Line 17: @@
 === Description ===
 "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."
-More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
 === Running Program ===
@@ Line 60: / Line 79: @@
 <pre  class="gcommand">
 ml PAML/4.9h-foss-2016b
-which baseml
+cd /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin
-/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml
+ls
 </pre>

Yhuang at 19:26, 10 August 2018

2018-08-10T19:26:23Z

← Older revision		Revision as of 15:26, 10 August 2018
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	=== Description ===		=== Description ===
	"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."		"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."
	More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]		More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]

Yhuang at 18:04, 10 August 2018

2018-08-10T18:04:53Z

← Older revision		Revision as of 14:04, 10 August 2018
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	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=PAML.%j.out<br>		<nowiki>#</nowiki>SBATCH --output=PAML.%j.out<br>
			<nowiki>#</nowiki>SBATCH --error=PAML.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
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	<pre class="gcommand">		<pre class="gcommand">
	ml PAML/4.9h-foss-2016b		ml PAML/4.9h-foss-2016b
	~~which baseml~~ which baseml		which baseml
	/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml		/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml

Yhuang at 17:44, 10 August 2018

2018-08-10T17:44:17Z

← Older revision		Revision as of 13:44, 10 August 2018
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	The last version of this application is at /usr/local/apps/eb/PAML/4.9h-foss-2016b		The last version of this application is at /usr/local/apps/eb/PAML/4.9h-foss-2016b

	To use this version, please ~~loads~~ the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml PAML/4.9h-foss-2016b		ml PAML/4.9h-foss-2016b
	</pre>		</pre>

	Here is an example of a shell script, sub.sh, to run on at the batch queue:		Here is an example of a shell script, sub.sh, to run on the batch queue:

	<div class="gscript2">		<div class="gscript2">