[Bioperl-l] FW: Pal2Nal problem

[Roy Chaudhuri]

Hi Xinli,

You don't need to use Bio::AlignIO to read $alnDP, since it is already a 
Bio::SimpleAlign object. To write out the Phylip file you just need this:

#output the result with phylip format

my $out = Bio::AlignIO->new(-file   => ">out.phy" ,
                             -format => 'phylip');
$out->write_aln($alnDP);


Hope this helps,
Roy.

On 15/04/2011 00:52, Sun, Xinli wrote:
>
> Dear Sir or Madam,
>
> I am a Perl beginner, and am using the
> Bio::Tools::Run::Alignment::Pal2Nal module to get the nucleotide
> sequences based on an alignment of their translations for PAML-yn00.
> However, I meet some problems, and send my codes and error report to
> you, and expect to get your help. The errors usually occur at the
> input of the DNA sequences and the output of the result. I am not
> sure for these.
>
> Do you have some examples with the sequence input and output for the
> Pal2Nal module? If yes, I hope to imitate your codes.
>
> Thanks a lot,
>
> Xinli Sun. Ph. D.
>
> Plant Science Department South Dakota State University SNP 211, Box
> 2140C Brookings, SD 57007 605-688-4984 (lab)
>
>
>
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