Difference between revisions of "PAML"
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other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. | other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. | ||
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| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CTL - sample .ctl files directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EX - examples directory |
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 20:12, 12 August 2022
Description
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. PAML is not suitable for building trees. It may be used to estimate parameters and test hypotheses to study the evolutionary process when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
Environment Modules
Run module spider paml to find out what environment modules are available for this application.
System Variables
- HPC_PAML_DIR - installation directory
- HPC_PAML_BIN - executable directory
- HPC_PAML_CTL - sample .ctl files directory
- HPC_PAML_DOC - documentation directory
- HPC_PAML_EX - examples directory
Additional Information
Most of the binaries in this package require appropriate .ctl files. Copy sample .ctl files from the $HPC_PAML_CTL directory to your working directory and modify them before running the programs. There are sample datasets in $HPC_PAML_EX.