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 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