I suspect that your failure to put the code in your question in a code block is the reason people are finding you hard to answer.

      if($tmp[0] eq ">") {
        my $nm = substr($line,1);
        $nm = $nm . $tot;
        $tot++;
        $line = <$IFH>; #IS THIS THE LINE YOU MEANT ?
        chomp $line;
        $ret{$nm} = $line;
      }
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If my guess is correct it means exactly the same as the same code in the while ($line = <$IFH>){ line that surrounds the read.

It reads the next line into the $line variable (If not end of file) within a block which is only run if the previous line began with a ">" character.