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>seq9
---KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
-----------------------------------------------
...
>seq3
-MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK-
-----------------------------------------------

use strict;
use warnings;

...
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}

UNIVERSAL->import is deprecated and will be removed in a future perl a
+t C:/Perl6
4/site/lib/Bio/Tree/TreeFunctionsI.pm line 94.
(seq0:0.04012,(seq2:0.06428,(seq4:0.22277,seq3:0.00000):0.14038):0.055
+06,(seq1:0
.08162,((seq9:0.71067,seq6:0.16093):0.24442,(seq5:0.28833,(seq10:0.127
+18,(seq7:0
.06605,seq8:0.08745):0.01099):0.42868):0.01353):0.15249):0.00931);