RAxML

Version 7.0.4 is the last version, located at /usr/local/RAxML/RAxML-7.0.4
Shortcut /usr/local/RAxML-latest is linked with Version 7.0.4 now .

Please refer to pdf file for detail commands

/usr/local/RAxML-latest raxmlHPC-MPI -# numberOfRuns -s sequenceFileName -n outputFileName -m substitutionModel -b bootstrapRandomNumberSeed

The script submitted to the queue, also refer to submit jobs to queues at rcluster,IOB

#!/bin/bash
cd working_directory
echo $LSB_HOSTS
cat /dev/null > mlist.$$
for variable in $LSB_HOSTS; do
     echo $variable >> mlist.$$
done
mpirun -np 2 -machinefile mlist.$$ /usr/local/RAxML-latest raxmlHPC-MPI < -# numberOfRuns -s sequenceFileName -n outputFileName -m substitutionModel -b bootstrapRandomNumberSeed [other options]> myoutput
rm -f mlist.$$

Then submit the job as:

bsub -n 2 -q queuename -o test.%J.out -e test.%J.err ./subp.sh

There are two more perl scripts tools

Frist one, it will automatically determine the best-scoring AA substitution model on a fixed starting tree.
For unpartitioned datasets execute it as following. The outfile will then contain the best-scoring AA model to use with RAxML.

perl /usr/local/RAxML-latest/ProteinModelSelection.pl alignmentFile.phylip > outfile

For partitioned datasets execute it as following. The outfile will then contain the best-scoring AA model for every partition.

perl /usr/local/RAxML-latest/ProteinModelSelection.pl alignmentFile.phylip partitionData.txt > outfile

The second perl script will convert FASTA files to RAxML’s relaxed PHYLIP format, i.e., not truncate sequence names. It will generate a file alignment.fasta.phylip that can be read by RAxML.

perl /usr/local/RAxML-latest/fasta2relaxedPhylip.pl alignment.fasta