[Bioperl-l] create Bio::AlignIO object from hash

Roy Chaudhuri roy.chaudhuri at gmail.com
Mon Jan 11 08:40:33 EST 2010

Hi Adam,

I'm guessing you actually want to create a Bio::SimpleAlign object 
(representing an alignment), rather than a Bio::AlignIO object (which is 
just for reading/writing alignment files). Bio::SimpleAlign has a 
documented new method that allows you to construct an alignment from 
Bio::LocatableSeq objects, which are similar to Bio::Seq objects but 
include gaps and start/end coordinates to describe their relationship to 
other sequences in the alignment.


On 11/01/2010 12:21, Adam Witney wrote:
> Hi,
> I am writing a script to automate the running of Phylip Pars. In the
> process i have to create a Bio::AlignIO object from a set of data
> that i have in a hash.
> I could write the hash data into a phylip file and then load the
> Bio::AlignIO from that file, but i wondered if i could skip the
> writing and then reading of a temporary file ?
> thanks for any help
> adam _______________________________________________ Bioperl-l
> mailing list Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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