#format can be mase, molphy, clustal, fasta or phylip
format mase

#models can be day, jtt, rev, nucjc, aaJC
model jtt

#AA or DNA
alphabet 20

#un-comment if you want to use gamma in the learning process
#gamma
#alpha 0.3

#un-comment if you only want to compute the branch lengths of a given tree
#bblonly

#input file
seqfile seq.txt
#output file
outfile run.out

#un-comment and add tree file for know tree (or starting point)
#treefile tree.txt