Difference between revisions of "RADICAL"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|radical}} | |{{#vardefine:app|radical}} | ||
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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==System Variables== | ==System Variables== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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. | |
|}} | |}} | ||
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__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:24, 6 December 2019
Description
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