__DATA__
Group 1
name
Group 2
name
Group 3
name
name
Group 4
name
Group 5
name
name
name
Group 11
name
name
Group 15
name
name
name
[download]

I guess it would have helped if I was more specific in exactly what my file looks like. Sorry about that. In reality, there are thousands of groups and my input file looks like this:

>Group 42
0    25ap, >name_06-T_1_0... at 92.00%
1    28ap, >name_06-T_1_0... *

>Group 43
0    28ap, >name_07-N_1_0... *

>Group 44
0    29ap, >name_07-N_1_0... *

>Group 45
0    25ap, >name_03-T_1_0... *
1    25ap, >name_06-T_1_0... at 100.00%
2    25ap, >name_07-N_1_0... at 100.00%
3    25ap, >name_11-N_1_0... at 100.00%
4    25ap, >name_14-T_1_0... at 100.00%
[download]

I would want an output that looks like this:


>Group 42
0    25ap, >name_06-T_1_0... at 92.00%
1    28ap, >name_06-T_1_0... *

>Group 45
0    25ap, >name_03-T_1_0... *
1    25ap, >name_06-T_1_0... at 100.00%
2    25ap, >name_07-N_1_0... at 100.00%
3    25ap, >name_11-N_1_0... at 100.00%
4    25ap, >name_14-T_1_0... at 100.00%
[download]

Yes, it is necessary to see exactly what your file looks like. Could have saved some typing knowing that :-)

A possible solution is close to my first answer.

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

{
    local ($/, $\) = ('', "\n\n");
    while (<DATA>) {
        chomp;
        print if tr/\n// > 1;
    }   
}


__DATA__
>Group 42
0    25ap, >name_06-T_1_0... at 92.00%
1    28ap, >name_06-T_1_0... *

>Group 43
0    28ap, >name_07-N_1_0... *

>Group 44
0    29ap, >name_07-N_1_0... *

>Group 45
0    25ap, >name_03-T_1_0... *
1    25ap, >name_06-T_1_0... at 100.00%
2    25ap, >name_07-N_1_0... at 100.00%
3    25ap, >name_11-N_1_0... at 100.00%
4    25ap, >name_14-T_1_0... at 100.00%
[download]

The statement local ($/, $\) = ('', "\n\n");, sets the INPUT_RECORD_SEPARATOR, $/, to read in paragraphs. A paragraph is lines of text followed by 1 or more blank lines, (2 or more newlines). The OUTPUT_RECORD_SEPARATOR, $\, is set to "\n\n". $\ is printed at the end of every print statement.