UGENE Forum - Alignment/Phylogeny

Nov 7^th, 2011 at 11:13pm

Alvarenga Offline
YaBB Newbies

Posts: 14

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!

Back to top

IP Logged

Reply #1 - Nov 8^th, 2011 at 11:58am

belinavones1 Offline
YaBB Newbies

Gender:
Posts: 1

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

~

Back to top

IP Logged

Reply #2 - Nov 8^th, 2011 at 2:13pm

Yuriy Vaskin Offline
Global Moderator

Gender:
Posts: 138

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).

Back to top

IP Logged

Reply #3 - Nov 8^th, 2011 at 7:25pm

Alvarenga Offline
YaBB Newbies

Posts: 14

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!

Back to top

IP Logged

Reply #4 - Nov 8^th, 2011 at 8:01pm

Mikhail Fursov Offline
YaBB Administrator

Gender:
Posts: 162

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?

---
UGENE team

Back to top

IP Logged

Reply #5 - Nov 9^th, 2011 at 1:05pm

Yuriy Vaskin Offline
Global Moderator

Gender:
Posts: 138

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

Back to top

IP Logged

Reply #6 - Nov 9^th, 2011 at 8:21pm

Alvarenga Offline
YaBB Newbies

Posts: 14

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

Back to top

IP Logged

Reply #7 - Jul 26^th, 2013 at 1:26pm

calvin Offline
YaBB Newbies
usa

Gender:
Posts: 1

Mikhail Fursov wrote 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?

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

steel fabrication Townsville

Back to top

IP Logged

	Welcome, Guest. Please Login or Register
	Welcome to our forum.