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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Alignment/Phylogeny https://forum.ugene.net/forum/YaBB.pl?num=1320682432 Message started by Alvarenga on Nov 7^th, 2011 at 11:13pm

Title: Alignment/Phylogeny
Post by Alvarenga on Nov 7^th, 2011 at 11:13pm

Hi!

The UGENE manual says that it supports reading and writing the nexus multiple alignment format. I haven't tried opening a .nex/.nxs file, but when I tried to export an alignment to this format it said I should send a feature request, so here I am! :)

Also, I would like to request more phylogenetic features. Are there any plans to support Minimum Evolution, Maximum Parcimony, and (specially) Maximum Likelihood algorithms? I think these are very important phylogenetic tools which are lacking in this great FOSS software and together with more editing options in the tree viewer they would really make UGENE more complete.

Thank you!

Title: Re: Alignment/Phylogeny
Post by belinavones1 on Nov 8^th, 2011 at 11:58am

.nex/.nxs files are behave like a puzzle i helpless even after lots of attempts to open files.

Title: Re: Alignment/Phylogeny
Post by Yuriy Vaskin on Nov 8^th, 2011 at 2:13pm

Hello! Thank you for your requests and interest in our project.
1) In UGENE 1.10 we’ve implemented MrBayes method. The algorithm uses writing the nexus alignment format, therefore it has been unlocked. Actually we locked the nexus writing due to complexity of the format, as it was said, and we steel can’t write trees and other stuff in the format but with alignments it’s ok. To use writing the nexus format you could download development version of UGENE 1.10 form here: http://ugene.unipro.ru/snapshot.html or you could wait till the official release of 1.10 which is coming soon.
2) About the trees. You could check our MrBayes method which I’ve mentioned. It also refers to inference of probability distribution like Maximum Likelihood method. We’ve planed a couple of features with trees editing. And that’s a good idea to implement a maximum parsimony method. I’ve created an issue about that (https://ugene.unipro.ru/tracker/browse/UGENE-690).

Title: Re: Alignment/Phylogeny
Post by Alvarenga on Nov 8^th, 2011 at 7:25pm

Mr.Bayes' Bayesian Inference is a wonderful addition, but I still would like to request attention to Maximum Likelihood, even if this can't be considered right now and it has to be delayed to the future. The reason for this is because in the field in which I work (microbial evolution) complementary trees produced with different algorithms are usually recommended by journals, so a Bayesian/ML approach is a very common one.

Maybe UGENE could try incorporating the GPLed PhyML? (http://www.atgc-montpellier.fr/phyml/binaries.php)

But those are really great news! Thanks for your efforts!

Title: Re: Alignment/Phylogeny
Post by Mikhail Fursov on Nov 8^th, 2011 at 8:01pm

Alvarenga,
This week we are focusing to close all issues in the 1.10 release and make it finally public.
I think we must plan the features you mentioned to 1.11 and, of course, make them available for beta testing asap with development snapshot.

Yuriy?

Title: Re: Alignment/Phylogeny
Post by Yuriy Vaskin on Nov 9^th, 2011 at 1:05pm

Ok, I've planed the issue on 1.11 (https://ugene.unipro.ru/tracker/browse/UGENE-693).

Title: Re: Alignment/Phylogeny
Post by Alvarenga on Nov 9^th, 2011 at 8:21pm

Ok, I'll look forward to the 1.11 beta. Thank you for your attention! All the best!

Title: Re: Alignment/Phylogeny
Post by calvin on Jul 26^th, 2013 at 1:26pm

Mikhail Fursov wrote on Nov 8^th, 2011 at 8:01pm:

Well that's great! if all the issues of 1.10 release and its should be done.....
for now I download 1.11. ::)