I can't really improve on FunkyMonk's solution, but it might be worthwhile to show how a data structure (hash-of-hashes-of-hashes, aka HoHoH) could be used. The following assumes that the data could include rows that are complete duplicates, and/or rows having the same key and the same "evalue", but different values in the middle columns.

The output will exclude duplicate data (that's what hashes are for); in the case of distinct rows having the same key and evalue, all rows will be included in the "combined" file, and the one with the (ascii-betically) lowest value in column two will be printed to the "lowest" file (you might want to modify that, by controlling how the sort is done in the innermost "for" loop). 

#!/usr/bin/perl
use strict;
use warnings;

my %data;
while ( <DATA> ) {
    my ( $key, $fields, $evalue ) = ( /^(\S+)\s+(.*?\s(\S+))\s*$/ );

    $data{$key}{$evalue}{$fields} = undef;
}

open my $f1, ">", "combined.data" or die $!;
open my $f2, ">", "lowest.data" or die $!;

for my $key ( sort keys %data ) {
    my $combined = "";
    my $printed_lowest = 0;
    for my $evalue ( sort {$a<=>$b} keys %{$data{$key}} ) {
        for ( sort keys %{$data{$key}{$evalue}} ) {
            $combined .= "\t$_";
            print $f2 "$key\t$_\n" unless ($printed_lowest++);
        }
    }
    print $f1 "$key$combined\n";
}

__DATA__
Q3KIL4_PSEPF    ONE    134    380    1    252    216.3    6.3e-64
Q3M236_ANAVT    TWO    107    563    1    468    203.2    5.3e-60
Q3M236_ANAVT    THREE    250    494    1    277    219.1    8.6e-65
Q3M5F5_ANAVT    FOUR    296    608    1    355    166.2    7.4e-49
Q3M5F5_ANAVT    FIVE    299    584    1    304    188.2    1.7e-55
Q3M7Z1_ANAVT    SIX    51    181    1    140    99.0    1.2e-28
Q3MAD2_ANAVT    SEVEN    107    508    1    468    350.1    3.3e-104
Q3MAD2_ANAVT    EIGHT    230    457    1    277    201.1    2.3e-59
Q3MBT3_ANAVT    NINE    203    606    1    468    102.5    1.1e-29
Q3MBT3_ANAVT    TEN    326    559    1    277    221.6    1.6e-65
Q3MBT3_ANAVT    ELEVEN    134    333    1    234    -334.1    2.7e-44
Q3MD63_ANAVT    TWELVE    173    491    1    355    248.5    1.2e-73

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In reply to Re: how to combine? by graff
in thread how to combine? by Anonymous Monk

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