Difference between revisions of "RADICAL"

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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:Phylogenetics]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|radical}}
 
|{{#vardefine:app|radical}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
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RADICAL stands for Random Addition Concatenation Analysis. It concatenates randomly selected gene partitions and builds phylogenetic trees (MP with PAUP*/ML with RAxML) to examine tree-to-tree agreement of the concatenation path. Also calculates ML support per node and partition. See Narechania et al. (2011 Genome Biol Evol).
 
RADICAL stands for Random Addition Concatenation Analysis. It concatenates randomly selected gene partitions and builds phylogenetic trees (MP with PAUP*/ML with RAxML) to examine tree-to-tree agreement of the concatenation path. Also calculates ML support per node and partition. See Narechania et al. (2011 Genome Biol Evol).
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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The radical/0.2 code is preset for using 2 RAxML threads, so the batch job resource request must be in the form of "nodes=1:ppn=2". There is no PAUP option.
 
|}}
 
|}}
 
<!--PBS scripts-->
 
<!--PBS scripts-->

Latest revision as of 21:28, 21 August 2022

Description

radical website  

RADICAL stands for Random Addition Concatenation Analysis. It concatenates randomly selected gene partitions and builds phylogenetic trees (MP with PAUP*/ML with RAxML) to examine tree-to-tree agreement of the concatenation path. Also calculates ML support per node and partition. See Narechania et al. (2011 Genome Biol Evol).

Environment Modules

Run module spider radical to find out what environment modules are available for this application.

System Variables

  • HPC_RADICAL_DIR - installation directory

Additional Information

The radical/0.2 code is preset for using 2 RAxML threads, so the batch job resource request must be in the form of "nodes=1:ppn=2". There is no PAUP option.