Here is a solution using Data::Table. However, I was a bit surprised to discover that the helper functions (such as fromFile, fromCSV, etc.) of Data::Table do not seem to support using regular expressions as a delimiter. For the data you posted, I would have used \s+ as the delimiter. By the time I discovered this, I had already written this solution...so I thought I'd post it. A solution like this will work if your input files are tab delimited (or one could use fromCSV for files with other delimiters).

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Table;

my @files = qw( input1.txt input2.txt input3.txt );
my @tables;
foreach my $file (@files) {
    my $dt = Data::Table::fromTSV($file, 1);
    push @tables, $dt;
}

my $merged_table;
TABLE:
    foreach my $i (0..$#tables){
        if ($i == 0){
            $merged_table = $tables[0]; 
            next TABLE;
        }
        $merged_table = $merged_table->join($tables[$i], Data::Table::
+INNER_JOIN, ['freq'], ['freq']);
    }

$merged_table->sort('freq', 1, 0);

open my $output_fh, ">", "combined.txt" or die "Cannot open combined.t
+xt: $!\n";
print {$output_fh} $merged_table->tsv;
$output_fh->close;

exit;
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