Difference between revisions of "Bamm"

Revision as of 16:10, 27 May 2022

Description

BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees.

BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BAMM and associated methods have been described and extended in several publications (PLoS ONE 2014 , Nature Communications 2013 , Systematic Biology 2014, and Evolution 2015). BAMM is a command line program written in C++. Post-run analysis and visualization is performed using the R package BAMMtools.

Required Modules

Serial

gcc/5.2.0
bamm

System Variables

HPC_BAMM_DIR - installation directory

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]]
+[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
-|{{#vardefine:app|Bamm}}
+|{{#vardefine:app|bamm}}
-|{{#vardefine:url|http://bamm-project.org/download.html}}
+|{{#vardefine:url|http://bamm-project.org/}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
 |{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-A program for multimodel inference on speciation and trait evolution.
+BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees.
+BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BAMM and associated methods have been described and extended in several publications (PLoS ONE 2014 , Nature Communications 2013 , Systematic Biology 2014, and Evolution 2015). BAMM is a command line program written in C++. Post-run analysis and visualization is performed using the R package BAMMtools.
 <!--Modules-->
-==Environment Modules==
+==Required Modules==
-Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+===Serial===
+* gcc/5.2.0
+* {{#var:app}}
+<!--
+===Parallel (OpenMP)===
+* intel
+* {{#var:app}}
+===Parallel (MPI)===
+* intel
+* openmpi
+* {{#var:app}}
+-->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 35: / Line 48: @@
 |}}
-<!--Job Scripts-->
+<!--PBS scripts-->
-{{#if: {{#var: job}}|==Job Script Examples==
+{{#if: {{#var: pbs}}|==PBS Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
 |}}
 <!--Policy-->