On Thu, Nov 18, 2010 at 2:31 PM, Bryan Lepore <span dir="ltr"><<a href="mailto:bryanlepore@gmail.com" target="_blank">bryanlepore@gmail.com</a>></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">
I am checking out sculptor, looks pretty cool, but I provided what i<br>
thought was a clustal format alignment to sculptor using --verbose,<br>
and it reports<br>
<br>
"Sorry: Wrong alignment format:"<br>
<br>
that's it. sounds like user error, but i'm not sure where to proceed<br>
next. i tried mafft and clustalw2 output for this. a sample of a bit<br>
of the top of the .aln is below.<br>
<br>CLUSTAL format alignment by MAFFT L-INS-i (v6.833b)<br>
<br>
<br>
gi|16132042|ref --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI<br>
gi|157163695|re --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI<br></blockquote><div><br></div><div>I just looked at the parser code, and I think it is expecting exactly the same output as CLUSTALW, which has a slightly different first line than MAFFT. �We now distribute a multiple sequence alignment program called MUSCLE with Phenix - you can use it like this:</div>
<div><br></div><div>phenix.muscle -in seqs.fa -out seqs.aln -clwstrict</div><div><br></div><div>I hope this fixes it - if not, Sculptor should also take alignments in FASTA or PIR format. �(Make sure you use the correct file extension, because this is what it uses to decide how to parse a file.)</div>
<div><br></div><div>-Nat</div></div>