Yes, trees in Jalview are calculated only based on marked positions.
For accuracy, I would not use phylogenetic tools from Jalview.
I would rather do the following:
1) Select the positions in Jalview.
2) Copy them.
3) Paste them as new alignment.
4) Save the alignment in a new file.
And then I use FastTree or RAxML (or even PhyML if you have access to
good computer cluster).
Romain
On 05/11/2014 20:18, James Starlight wrote:
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]
<mailto:[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
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--
Romain Studer
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel:+44 (0)1223 492 547 <tel:%2B44%20%280%291223%20492%20547>
Twitter: @RomainStuder
--
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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