I am trying to construct a phylogenetic tree by using RAxML software.
These are my fist tries, so my knowledge is a little bit limited.
I run the following command:
raxmlHPC-SSE3 –f i -s all_sheep_mt.phylip -n boot -m GTRGAMMA -b 12345 -p 123456 -# 1000
and RAxML generated the file with all the 1000 trees (RAxML_bootstrap. boot).
I also run the previous command without the -b parameter and I took each tree on a different file and a file with the best one (RAxML_bestTree.boot).
finally, I run the following command in order to have except the branch lengths and the the bootstrap values (percentage of confidence).
raxmlHPC-SSE3 –f b -m GTRGAMMA -s all_sheep_mt.phylip -z RAxML_bootstrap.boot -t RAxML_bestTree.boot -n bootTree
The problem is that I finally have only the branch lengths onto the tree.
Any idea what I'm doing wrong?
Thank you very much in advance,