|MUSCLE manual > tree output files|
|Guide tree output files|
Using a precomputed guide tree
Making a N-J or UPGMA tree from a multiple alignment
You can save the guide tree from the first and/or second
iteration using the -tree1 and -tree2 options,
The trees are saved in Newick (PHYLIP-compatible) format.
These should not be considered high-quality phylogenetic trees, though they may be useful as a fast way to get approximate evolutionary relationships between some new sequences:
muscle -in seqs.fa -out seqs.afa -tree1 first.phy -maxiters 1
You can make a
neighbor-joining tree if you want a better estimate of the true phylogeny.