On 30/05/2012 14:54, Petr Efler wrote:
As far as I understand it, there are all sequences in a dataset
compared to each other during construction of the multiple alignment
by ClustalW.
That's roughly correct - though it depends on the parameters passed to
clustalW as to how the comparison is done.
Is there a possibility to get a list of %-identities generated during
the pairwise alignments? Thanks!
Jalview doesn't recover any of the pairwise scores generated by the
ClustalW service at the moment - the JABAWS service doesn't provide
them, and I'm slightly embarrassed to say that there is also no menu
option in Jalview 2.7 that allows you access to the matrix of pairwise
percentage identities computed when you ask it to build a percentage
identity based tree. You do get a pairwise score if you pick two or more
sequences and select 'Pairwise alignments' - but the alignment report
isn't particularly easy to read if you have lots of sequences.
If you need it desperately, its fairly easy to create a groovy script
that would dump pairwise percentage identities, or you could head over
to the ClustalW server at EBI, run the alignment again, and download the
similarity matrix that is produced along with the alignment and guide tree.
Sorry about that - it always seems I have something I need to do before
I can create the 'export pairwise similarity matrix' menu item :(
Jim.
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