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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