ID1      ID2      dN     dS     Omega   Label_ID1       Label_ID2       Group
AVP78042 AVP78031 0.0059 0.1188 0.0500  SARSr-bat-CoV   SARSr-bat-CoV   Intra
ATO98108 AVP78031 0.1373 1.4673 0.0936  SARSr-bat-CoV   SARSr-bat-CoV   Intra
ATO98108 AVP78042 0.1371 1.4224 0.0964  SARSr-bat-CoV   SARSr-bat-CoV   Intra

##</code><code>##

 
Distance    ID_1        ID_2        Value
DISTANCE    AVP78042.1  ATO98108.1  0.29731
DISTANCE    AVP78042.1  ATO98120.1  0.29281
DISTANCE    AVP78042.1  ATO98132.1  0.33095

##</code><code>##

use strict;
use warnings;
use feature qw{ say };

sub load {
    my ($file, $table, $phase) = @_;
    open my $in, '<', $file or die "$file: $!";
    while (<$in>) {
        chomp;
        my @columns = split /\t/;
        my $id = join '_', @columns[0, 1];
        die "Duplicate $id."
            if 'first' eq $phase && exists $table->{$id};

        push @{ $table->{$id} }, $columns[2];
        say join "\t", @columns[0, 1], @{ $table->{$id} }
            if 'print' eq $phase;
    }
}

my %table;
my $phase = 'first';
while (my $file = shift @ARGV) {
    load($file, \%table, $phase);
    $phase = 1 == @ARGV ? 'print' : '';
}

##</code><code>##

ID1          ID2         dN          dS          Omega   Value   Label_ID1       Label_ID2       Group
AVP78042     AVP78031    0.0059      0.1188      0.0500 0.29731  SARSr-bat-CoV   SARSr-bat-CoV   Intra
ATO98108     AVP78031    0.1373      1.4673      0.0936    -     SARSr-bat-CoV   SARSr-bat-CoV   Intra