[Bioperl-l] Clustal w - fixed width characters

[Tariq Shafi]

Hi

I am using a Clustalw alignment and in doing the alignment I want to format 
my alignment results in fixed width characters.

I get an object called $alignment from the Clustalw operation, using 
Bio::Tools::Run::Alignment::Clustalw;

Later on, I am using the following code:

foreach $seq ($alignment->each_seq) {
    print b($seq->id(), ':');
    $str = $seq->seq();
    print $str, br();
    }

This gives alignments but they are difficult to visualise as the characters 
are not of fixed width, so (visually only) it is out of sync. How do I make 
the characters in each sequence of fixed width?

Regards

Tariq

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