also I'll very thankful if someone suggest me some server for the simple comparison of 2 phylogenetic trees and cluster calculations
James 2014-11-05 21:18 GMT+01:00 James Starlight <[email protected]>: > 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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