<p>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?</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>Thank you for any help you can offer Biostars folks.</p>

<p>Zev referred me to this question, which provided me the impetus for registering on Biostars.</p>

<p>As he mentioned, PAUP* is now open source. However, I cannot find where Dave Swofford was posting the change log. The worst part is that I know I&#39;ve been there before - I recall him saying that Sinauer will have the license for the GUI but the command-line version will be free, which is what you want. I posted a comment to Zev&#39;s response because I was still looking for the URL; I&#39;ll post it if I can find it (perhaps it&#39;s down right now?).</p>

<p>Anyway, you may consider R. Klaus Schliep&#39;s phangorn library (<a href="http://cran.r-project.org/web/packages/phangorn/phangorn.pdf">http://cran.r-project.org/web/packages/phangorn/phangorn.pdf</a>) will estimate phylogenies using MP as an optimality criterion. If you need a complete command-line interface for some other stuff in a pipeline, I recommend writing a script and calling it using</p>

<pre>
Rscript --vanilla your_script.R [arguments]</pre>

<p>When called this way, R, like other languages, will accept command-line arguments.</p>

<p>Hope this helps!</p>

<p>[Edit: typos]</p>
