Hi Hiren,
In principle it should be possible to convert individual LCBs to a
phylip for phylogenetic inference, or to concatenate all LCBs into a
single alignment, or extract just the backbone segments as commonly done
in the Mauve+ClonalFrame workflow.
As for the file formatting details & errors, that looks to me like a
discussion you would need to have between the BioPerl list and the RAxML
list. It has nothing to do with Mauve.
Best,
-Aaron
On Wed, 2015-08-19 at 17:55 +0200, Hiren Ghosh wrote:
> Hello all,
> I was having a try to convert mauve XFMA file to phylip format for
> further run on RaxML to draw a MLH tree. I
> used bioperl to convert the file in such way
>
> use Bio::AlignIO;
>
> $in = Bio::AlignIO->new(-file => "test.xmfa" ,
> -format => 'xmfa');
> $out = Bio::AlignIO->new(-file => ">test",
> -format => 'phylip');
>
> while ( my $aln = $in->next_aln ) {
> $out->write_aln($aln);
> }
>
>
>
> and next step i used
>
>
> $ ./raxmlHPC -s Test_aln -m GTRCAT -n Test -p 12345
>
> RAxML correctly finished parsing your PHYLIP file,
> but there seems to be garbage at the end of the file, i.e.,
> non-whitespace characters!
> RAxML will exit now
>
>
>
> End of the aln file looks like this
>
> GTTCGGTGAG TGGCTCCGCC ACGACATCCT TTCCGGAACG TTCGAGCCTG
> CCGTTCTGGA
>
> TCACGATCTT GCGATTTTGC TGACCAAGGC GAGGCAACAC AGCCTTGCGC
> TTCTAGGCCC
>
> ATCCGCAGCC ACGTTTTTCG AGCCGGTGCC GAAGGAGCAT TTCTCCAAGG
> CGCTTTTCGA
>
> CACTATTGCC CAGTGGAATG CAGAGTCGGA TTGGAAGGGT GACGAGCGGA
> ACGTCGTTCT
>
> TGCTCTTGCT CGCATTTGGT AC
>
> Kindly help me out.
>
> Thanks advance.
>
> Best
>
>
> Hiren
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
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