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,
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-
