>seq9
---KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
-----------------------------------------------
>seq7
----SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKK
MEKLNNIFF--------------------------------------
>seq8
----SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKK
MEKLNNIFFTLM-----------------------------------
>seq10
--FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKK
MEK--------------------------------------------
>seq6
--FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKK
LEKLSSTLLRSI-----------------------------------
>seq5
----SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKK
IEKLTTLLMR-------------------------------------
>seq4
------EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVS-YEMRLFGVQKD
NFALEHSLL--------------------------------------
>seq0
--FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKK
IEKF-------------------------------------------
>seq1
-KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKK
IEKFHSQLMRLMELKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKK
VEKLHGK----------------------------------------
>seq3
-MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK-
-----------------------------------------------

##</code><code>##

use strict;
use warnings;

use Bio::AlignIO;
use Bio::Align::ProteinStatistics;
use Bio::Tree::DistanceFactory;
use Bio::TreeIO;

my $alnio = Bio::AlignIO->new(-file => 'outfile.fasta', -format=>'fasta');

my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ');

my $stats = Bio::Align::ProteinStatistics->new;

my $treeout = Bio::TreeIO->new(-format => 'newick');

while( my $aln = $alnio->next_aln ) 
{
 my $mat = $stats->distance(-method => 'Kimura',
                            -align  => $aln);
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}


##</code><code>##

UNIVERSAL->import is deprecated and will be removed in a future perl at 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):0.05506,(seq1:0
.08162,((seq9:0.71067,seq6:0.16093):0.24442,(seq5:0.28833,(seq10:0.12718,(seq7:0
.06605,seq8:0.08745):0.01099):0.42868):0.01353):0.15249):0.00931);