Notung

[mstolzer]

Presenter: Maureen Stolzer

Link: http://www.cs.cmu.edu/~durand/Notung/

Brief description: Notung is a gene tree-species tree reconciliation software package that supports duplication-loss (DL) and duplication-transfer-loss (DTL) event models with a parsimony-based optimization criterion.

Notung offers a unified framework for incorporating event parsimony into phylogenetic tasks, including rooting an unrooted gene tree, rearranging of a rooted gene tree in areas of weak sequence support, and resolving a non-binary gene tree. Reconciliation with a non-binary species tree is also supported and avoids overestimating duplications in gene trees that are incongruent due to incomplete lineage sorting.

User interface: Notung-2.9 offers a graphical user interface that facilitates exploratory data analysis, as well as a command-line interface that supports analysis of a large number of gene trees automatically.

It produces a variety of information valuable to biologists and is easily accessible. Reports include information on the timing of events relative to species divergences; ancestral gene content; and identification of homology relationships (orthology, paralogy, and xenology).

[wrightaprilm]

Thank you, Maureen!

I have been tweeting small adverts for the Software Bazaar in the lead-up to the Evolution meetings. Both to draw interest from potential users to come visit, but also to encourage more software folks to file their issues early. Every year, almost all the participants open issues the day before the meeting, which is a bit to handle ;)

If you'd be OK with me tweeting a link to your software's website and from the iEvoBio twitter, let me know. It's totally optional.

[mstolzer]

That would be great! Thanks for setting this up. Best, Maureen Stolzer

…

----------------------------------- Postdoctoral Researcher Durand Lab Carnegie Mellon University Pittsburgh, PA USA [email protected]

On Mon, Jun 17, 2019 at 11:15 AM April Wright ***@***.***> wrote: Thank you, Maureen! I have been tweeting <https://twitter.com/iEvoBio/status/1133759949664903168> small adverts for the Software Bazaar in the lead-up to the Evolution meetings. Both to draw interest from potential users to come visit, but also to encourage more software folks to file their issues early. Every year, almost all the participants open issues the day before the meeting, which is a bit to handle ;) If you'd be OK with me tweeting a link to your software's website and from the iEvoBio twitter, let me know. It's totally optional. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#9?email_source=notifications&email_token=AL6L7VROVHQEED2KBZQPLN3P26TBXA5CNFSM4HYM3ZNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODX3P6PQ#issuecomment-502726462>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AL6L7VQ4FDNDMEFELUWGQ6LP26TBXANCNFSM4HYM3ZNA> .