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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