[phenixbb] sculptor

Nathaniel Echols nechols at lbl.gov
Thu Nov 18 14:47:53 PST 2010

On Thu, Nov 18, 2010 at 2:31 PM, Bryan Lepore <bryanlepore at gmail.com> wrote:

> I am checking out sculptor, looks pretty cool, but I provided what i
> thought was a clustal format alignment to sculptor using --verbose,
> and it reports
> "Sorry: Wrong alignment format:"
> that's it. sounds like user error, but i'm not sure where to proceed
> next. i tried mafft and clustalw2 output for this. a sample of a bit
> of the top of the .aln is below.
> CLUSTAL format alignment by MAFFT L-INS-i (v6.833b)
> gi|16132042|ref
> gi|157163695|re

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:

phenix.muscle -in seqs.fa -out seqs.aln -clwstrict

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.)

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