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bin/tree-clan-splitter.pl  view on Meta::CPAN

    }

    ### Checking clans layout...
    my ($is_included, $composition_for) = check_inclusions($clan_hash, \@ps_clans);
    my @main_clans = grep { ! %$is_included{$_} } @ps_clans;
    #### @main_clans

    # fit ali to ali2phylip filtering
    my $alifile  = $stripped_intree . '.ali';
    my $base_ali = Ali->load($alifile);
       $base_ali->dont_guess;
    my $alist = $tree->alphabetical_list;
    #### $list
    my $ali = $alist->filtered_ali($base_ali);

    my $n_ali;

    IDLIST:
    for my $main_clan ( @main_clans ) {

        $n_ali++;