Hi Romain, thank you very much for the explanation! I've already used TrimAl as the part of the Phylemon2 server and found it very useful :-) Regarding calculating Trees in JalView using subset of the residues: as I noticed the tree are calculated just in case when the positions of ligand-contacting residues are marked by red color in the top, aren't it? Is it possible in addition to check on what exactly subset trees has been calculated based on the output results? Finally regarding accuracy of the calculation of the trees- what method should produce best results for the alignment consisted of several hundred of sequences?
James 2014-11-05 16:59 GMT+01:00 rstuder <[email protected]>: > 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 > > > _______________________________________________ > Jalview-discuss mailing > [email protected]http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > > > > -- > 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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