[Bioperl-l] Trying to get a conservation index out of a MSA

[Brian Osborne]

Stephane,

Can you send an example input file and complete script? You only showed a part of the script before, I think.

Brian O.


On Feb 3, 2014, at 6:44 PM, Téletchéa Stéphane <stephane.teletchea at inserm.fr> wrote:

> Le 03/02/2014 22:39, Brian Osborne a écrit :
>> Stephane,
>> 
>> Do you see the same issue when "-displayname_flat => 1”?
>> 
>> I’m talking about when you create $aln.
>> 
>> Brian O.
> Hum, sorry, forget about the duplicates names,
> I should have done a proper verification, ...
> 
> There *are* duplicate names in my alignment, from the blast results
> I transform all pass in fasta sequences for muscle, since there are
> two pass -> two times the same sequence...
> 
> The other sequence stands true, though, I'm still getting
> a 100% conservation for each position altough for
> sure this is impossible to have such conservation amongst species
> for a given protein ...
> 
> Any help on the "get id per position" code I'm using?
> 
> Thanks again,
> 
> Stéphane
> 
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