my current code. Which currently produces the wrong output

What does the correct output look like? 



while (my $line = <F>) {
        chomp($line);
        <F>; # skip firts line of phylip

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That last line will skip every second line of the file (lines 2, 4, 6, 8, etc.)    If you only want to skip the first line then: 

<F>; # skip first line of phylip
while (my $line = <F>) {
        chomp($line);

[download]

In reply to Re: manipulating alignment data by jwkrahn
in thread manipulating alignment data by AWallBuilder

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