I would like to obtain the RAXML ML tree for each gene family. I have around 800 .phy trimmed alignments. I tried looping the .phy files to produce one tree each but somehow only one tree is produced in the end. Should I create sub-directories to store them or is there a better way to do this? I am specifically wanting to make single trees and hence the question.
So each gene family is named as
Ortho1.phy Ortho2.Phy ....
I tried using
for f in /home/Single_trees/trimmed_alignment/*.phy; do g=$(echo $f | sed 's/.phy$//g'); raxmlHPC -f a -x 100 -m PROTGAMMAAUTO -p 100 -s $f -N 100 -n $g.tree; done;
I wanted to name each tree based on the gene family name now but htis always gives me an error saying $ symbol is not allowed.