Difference between revisions of "RADICAL"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR
 
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{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:24, 6 December 2019

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).

Required Modules

Serial

  • radical

System Variables

  • HPC_RADICAL_DIR

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.




Validation

  • Validated 4/5/2018