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

Téletchéa Stéphane stephane.teletchea at inserm.fr
Mon Feb 3 23:44:12 UTC 2014

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,


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