Dear James,
For aligning the sequences, I would recommend MAFFT (L-INS-i) or
Clustal-Omega:
http://mafft.cbrc.jp/alignment/software/
http://www.clustal.org/omega/
Then, you can use Jalview to select manually the ligand-binding domain
in your alignment.
You can also use TrimAl to select only well aligned position that
corresponding to phylogenetic signal.
http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend
FastTree. It produces quite good results and is very easy to use:
http://www.microbesonline.org/fasttree/
There is also RAxML which is developed for big alignments:
http://sco.h-its.org/exelixis/web/software/raxml/index.html
Best regards,
Romain
On 05/11/2014 15:06, James Starlight wrote:
Dear JalView users!
I need to perform large-scale phylogenetic analysis of big dataset of
GPCR sequences selecting as the input only residues involved in the
ligand-binding site of those receptors (taken from the structural
data) from the input multiple-sequence alignment. I wounder what
method for phylogenetic trees calculation will be best (neighbourhood
joining or pairs-distance calculations) for my task as well as how to
make selection of the selecting residues properly (previously I've
done it by cntrl-left click on the bottom of the alignment marking
corresponded zone by red colour). On what additional details should I
paid my attention during such calculations in case when I'm dealing
with a very big number of sequences?
Thank you for the help,
James
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Romain Studer
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel: +44 (0)1223 492 547
Twitter: @RomainStuder
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