I am on the hunt for a maximum parsimony tree-building program with bootstrapping for Linux that one can parse options to easily from the command-line. Does anyone have any recommendations?
In brief, the tree-builder is to be run as a part of a shell script based pipeline that produces consensus trees for a given alignment under various conditions and finds the configuration that produces the consensus tree with the highest mean branch support value (thus the bootstrapping). My alignment has ~100 sequences of ~16kb, though these are quite highly conserved (parsimony informative sites are only a few hundred). As the earlier steps of the pipeline produce alignments in .fasta format it would be preferable that the tree-builder can read these.
I have been looking at TNT so far but find its interface rather unwieldy. The fact that it opens an interpreter when the program is called is sub-optimal as I would prefer that I can simply run the program with options from the command-line from the shell script (i.e. user$./program [options] [file]). This being said, if anyone has figured out how to use TNT like this then I would be grateful for your advice.
The other option I have looked at is PAUP* but I would prefer not to purchase this if there is a simpler program freely available.
Thank you for any help you can offer Biostars folks.