[Bioperl-l] Remove columns containing more than 75% gaps in an alignment

[Sendu Bala]

Daniel Gerlach wrote:
> Hello,
> 
> Is it possible to remove only columns containing e.g. more than 75% gaps 
> from an alignment? I was thinking at
> 
> $aln2 = $aln->remove_gaps('-'[,$all_gaps_columns])
> 
> This would allow me to remove all gaps or gap-only columns but not using 
> a threshold.

Well, you can use gap_col_matrix() to decide which columns you don't 
want, and then use remove_columns().