The following is a variation on the 'Schwartzian' transform (Ref: FAQ How do I sort an array by (anything)?.) Map your array into one that can be sorted easily, sort it, and extract the results.

use strict;
use warnings;
use Test::More tests=>1;
my @transcripts = qw(  t1  t1  t2  t2  t1  t2 );
my @alles       = qw(  a1  a2  a1  a2  a3  a3 );
my @effects     = qw( mis mis mis mis del del );

my @transpose_matrix
    = map { [shift(@transcripts), shift(@alles), shift(@effects)] } 0.
+.5;

my @sorted_transpose
    = sort{ $a->[0] cmp $b->[0] or $a->[1] cmp $b->[1] } @transpose_ma
+trix;

my @sorted_effects = map {$_->[2]} @sorted_transpose;

is_deeply( \@sorted_effects, [qw(mis mis del mis mis del)], 'sort by r
+ow');
[download]

UPDATE: Use of zip_by of List::UtilsBy allows the Schwartzian Transform to be coded in the usual way without any explicit loop.

use strict;
use warnings; use Test::More tests=>1;
use List::UtilsBy qw(zip_by);
my @transcripts = qw(  t1  t1  t2  t2  t1  t2 );
my @alles       = qw(  a1  a2  a1  a2  a3  a3 );
my @effects     = qw( mis mis mis mis del del );
my @matrix      = (\@transcripts, \@alles, \@effects);


my @sorted_effects
    = map {$_->[2]} 
        sort{ $a->[0] cmp $b->[0] or $a->[1] cmp $b->[1] }
            zip_by {[@_]}
                \@transcripts, \@alles, \@effects;

is_deeply( \@sorted_effects, [qw(mis mis del mis mis del)], 'sort by r
+ow');
[download]

Result:

1..1
ok 1 - sort by row
[download]

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