Applications/Beast - Revision history

Pysdlb: /* Non Interactive */

2022-11-22T10:03:50Z

‎Non Interactive

Pysdlb: /* Non Interactive */

2022-11-22T10:03:20Z

‎Non Interactive

Pysdlb at 11:12, 24 May 2019

2019-05-24T11:12:09Z

Pysdlb at 14:08, 18 April 2017

2017-04-18T14:08:12Z

Pysdlb: Pysdlb moved page Beast to Applications/Beast without leaving a redirect

2017-04-18T13:21:21Z

Pysdlb moved page Beast to Applications/Beast without leaving a redirect

Pysdlb at 13:18, 18 April 2017

2017-04-18T13:18:27Z

Pysdlb at 13:15, 18 April 2017

2017-04-18T13:15:57Z

Pysdlb: Created page with "TOC ==Application Details== * Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. * Version: 1.8.3 * Modules: beast/..."

2017-04-18T12:59:05Z

Created page with "__TOC__ ==Application Details== * Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. * Version: 1.8.3 * Modules: beast/..."

New page

__TOC__

==Application Details==

* Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
* Version: 1.8.3
* Modules: beast/1.8.3
* Licence: Free, open-source

==Usage Examples==

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

It can make use of highly-parallel processors such as those in 3D graphics boards (referred to as Graphics Processing Units or GPUs) found in many PCs. In general using it (even if not using a GPU) will improve the performance of BEAST. However, installing it for BEAST to use is not a simple operation presently (but we hope to fix this shortly) and it is not necessarily going to benefit all data sets. In particular, for the use of a GPU (and currently only NVidia ones are supported) to be efficient, long partitions are required (perhaps >500 unique site patterns).

===Interactive===

While logged into a reserved high memory node:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@c230 ~]$ module add beast/1.8.3
[username@c230 ~]$ module add libbeagle/2.1.2
[username@c230 ~]$ module add java/jdk1.8.0_102
[username@c230 ~]$ beast Random_Cratopus_BEAST.xml

</pre>

===Non Interactive===

Using a [[General/Slurm|SLURM script]] to run an array based processing beast processing script across the compute nodes:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

#!/bin/bash
#SBATCH -J Random_BEAST
#SBATCH -N 1
#SBATCH -o %A-%a.log
#SBATCH -e %A-%a.err
#SBATCH -p compute

module add beast/1.8.3
module add libbeagle/2.1.2
module add java/jdk1.8.0_102

for i in ${SLURM_ARRAY_TASK_ID}
do
cp Random_Cratopus_BEAST.xml Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}.xml
sed -i -e "s/Random_Cratopus_BEAST/Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}/g" Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}.xml
done

beast "Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}".xml

</pre>

==Further Information==

* [http://beast.bio.ed.ac.uk/ http://beast.bio.ed.ac.uk/]
* [http://beast.bio.ed.ac.uk/Tutorial_6 http://beast.bio.ed.ac.uk/Tutorial_6]
* [http://beast.bio.ed.ac.uk/Tutorial_8 http://beast.bio.ed.ac.uk/Tutorial_8]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

← Older revision		Revision as of 10:03, 22 November 2022
Line 55:		Line 55:


−	* Then submitting this to [[~~General~~/Slurm\|SLURM]].	+	* Then submitting this to [[Quickstart/Slurm\|SLURM]].

@@ Line 59: / Line 59: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-sbatch BeastDEMO.job
+[username@login01 ~]$ sbatch BeastDEMO.job
 Submitted job 345663
 </pre>

@@ Line 53: / Line 53: @@
 </pre>
 * Then submitting this to [[General/Slurm|SLURM]].
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

@@ Line 28: / Line 28: @@
 ===Non Interactive===
-Using a [[General/Slurm|SLURM script]] to run an array based processing beast processing script across the compute nodes:
+Using a [[FurtherTopics/Advanced_Batch_Jobs#Array_batch_job| SLURM script]] to run an array based processing beast processing script across the compute nodes:
 <pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
@@ Line 62: / Line 62: @@
 Submitted job 345663
 </pre>
 ==Further Information==

@@ Line 71: / Line 71: @@
 * [http://beast.bio.ed.ac.uk/Tutorial_8 http://beast.bio.ed.ac.uk/Tutorial_8]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

← Older revision	Revision as of 13:21, 18 April 2017
(No difference)

@@ Line 16: / Line 16: @@
 ===Interactive===
-While logged into a reserved high memory node:
+While logged into a reserved high memory node (''c230''):
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@c230 ~]$ module add beast/1.8.3
 [username@c230 ~]$ module add libbeagle/2.1.2
 [username@c230 ~]$ module add java/jdk1.8.0_102
 [username@c230 ~]$ beast Random_Cratopus_BEAST.xml
 </pre>
@@ Line 57: / Line 54: @@
 </pre>

Applications/Beast - Revision history

Pysdlb: /* Non Interactive */

Pysdlb: /* Non Interactive */

Pysdlb at 11:12, 24 May 2019

Pysdlb at 14:08, 18 April 2017

Pysdlb: Pysdlb moved page Beast to Applications/Beast without leaving a redirect

Pysdlb at 13:18, 18 April 2017

Pysdlb at 13:15, 18 April 2017

Pysdlb: Created page with "__TOC__ ==Application Details== * Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. * Version: 1.8.3 * Modules: beast/..."

Pysdlb: Created page with "TOC ==Application Details== * Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. * Version: 1.8.3 * Modules: beast/..."