Phylogenetic Analysis by Maximum Likelihood (PAML) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. 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.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load paml [user@cn3144 ~]$ baseml ... [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. paml.sh). For example:
#!/bin/bash set -e module load paml baseml ...
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] paml.sh
Create a swarmfile (e.g. paml.swarm). For example:
baseml ... baseml ... baseml ... baseml ...
Submit this job using the swarm command.
swarm -f paml.swarm [-g #] [-t #] --module pamlwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module paml | Loads the paml module for each subjob in the swarm |