RAxML generate best tree from 500 bootstrap trees

Question

[Wilber0x]

I am using RAxML. I want to make a single maximum likelihood tree based on 500 boostraps. I am also using partitions for my alignment.

I used this command in RAxML:

raxmlHPC-PTHREADS-AVX2 -m GTRGAMMA -p $RANDOM -x $RANDOM -N 500 -T 4 -s myAlignment.phy -q partitionSchemel.txt -n output.tre

I got two files for the output, one file called RAxML_info.output.tre, and one called RAxML_bootstrap.output.tre. RAxML_bootstrap.output.tre contains 500 individual trees for my data. How can I use this file of 500 trees to create a best scoring tree with associated bootstrap values?

How can I edit my command to automatically output a RAxML_bestTree.output.tre file?

Answer 1

[young_bioinformatician]

Check the -f parameter in the manual I attached. It may be -f a

RAxML Manual