UGENE Forum - How do I build a maximum parsimony tree?

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How do I build a maximum parsimony tree? (Read 4807 times)

Aug 17^th, 2019 at 8:00pm

morecoffee Offline
YaBB Newbies

Posts: 4

Hello all,
I am a student, so bear with me if I'm doing this wrong.

I have aligned some sequences and am looking to do a maximum parsimony tree, for example doing a branch & bound, but I can't find out how. Is this feature missing? Is there a workaround?

Also, I should try to remove uninformative characters before doing so, but can't find a way.

Any help?

Thanks!

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Reply #1 - Aug 19^th, 2019 at 12:19pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Hello,

Quote:

am looking to do a maximum parsimony tree

Unfortunately, this method is not yet integrated into UGENE.

If you'd like to build a tree using another method, see this page: https://ugene.net/wiki/display/UUOUM32/Building+Phylogenetic+Tree.

Quote:

I should try to remove uninformative characters before doing so, but can't find a way.

If you need to remove a region in an alignment, just select the region and click Delete on the keyboard. For other options of editing an alignment, see https://ugene.net/wiki/display/UUOUM32/Editing+Alignment.

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Reply #2 - Aug 20^th, 2019 at 1:58am

morecoffee Offline
YaBB Newbies

Posts: 4

Thanks. Should I open a feature request? I am not a programmer, but my guess is that it would take the external tools plugin and use it with something like Nona

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Reply #3 - Aug 20^th, 2019 at 12:08pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Quote:

Should I open a feature request?

We've already taken your feedback into account, however, you might create an issue in our issues tracking system, it's open for everyone.

Let me inform you that unfortunately the issue probably won't be implemented in the nearest UGENE versions in terms of free support. But the more feedbacks like this we have, the earlier the feature is going to be added into UGENE. So, thank you for the feedback anyway!

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Reply #4 - Aug 21^st, 2019 at 3:08pm