But then I want to sort alleles according to another array, let's say : my @alleles_origin = (a3,a2,a1);

See for example the replies to the thread How to Order an Array's Elements to Match Another Array's Element Order.

use warnings;
use strict;
use Data::Dump;

my @allel_order = qw/ a3 a2 a1 /;

my @matrix = (
    [qw/ t1 t1 t2 t2 t1 t2 /],
    [qw/ a1 a2 a1 a2 a3 a3 /],
    [qw/ mis mis mis mis del del /],
);

my %allel_order = map { $allel_order[$_] => $_ } 0..$#allel_order;
my @idx = sort { $matrix[0][$a] cmp $matrix[0][$b] or
    $allel_order{$matrix[1][$a]} <=> $allel_order{$matrix[1][$b]} }
    0..$#{$matrix[0]};
dd @idx;  # (4, 1, 0, 5, 3, 2)
my @out = map { $matrix[2][$_] } @idx;
dd @out;  # ("del", "mis", "mis", "del", "mis", "mis")
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