On Fri, Nov 19, 2010 at 4:22 AM, Jovine Luca <span dir="ltr">&lt;<a href="mailto:luca.jovine@ki.se">luca.jovine@ki.se</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

<div class="im">This is actually a bit odd, since one could run version 3.7 of MUSCLE with a -stable flag that would output sequences in the the same order as the input... but apparently this has been disabled in the version that ships with PHENIX (3.8.31). Maybe we could just ask Robert Edgar to put it back<font class="Apple-style-span" color="#888888">?</font></div>


</blockquote></div><br><div>Yeah, I&#39;ll ask him about this.  Unfortunately we needed a bug fix in 3.8, otherwise I might have left it alone.</div><div><br></div><div>But I still think the solution is to do the alignment internally - the user should be able to provide a PDB file and a target sequence, and the program will run MUSCLE automatically and figure out which row in the alignment output corresponds to each sequence.  This avoids an extra step and would clear up the confusion regarding formats, ordering, etc.</div>

<div><br></div><div>-Nat</div>