Abstract Detail



Conference Wide

Kandziora, Martha [1], Toscani Field, Jasper [2].

Automatic updating of phylogenies.

Adding new sequences to existing datasets can be tedious and time consuming. This workshop will be helpful for anyone looking to speed up their phylogenetic analyses. Here, we introduce two new tools that will help to update existing phylogenies. No matter if you have Sanger sequences or NGS data, updating phylogenies has never been easier and faster: use Physcraper (for Sanger sequences) or Phycorder (for NGS data). We will briefly introduce the way the tools work before we show how they can be used in a hands-on session. With Physcraper, new sequences of a focus clade are added to the dataset based on blast searches from Genbank or a local database. Phycorder requires closely related taxa to be added to an existing alignment. After updating the alignment, in both tools, the new sequences are placed onto the existing tree, which is then used as a starting tree for a Maximum Likelihood estimation. The advantage is that the method rapidly computes a new phylogeny including support values for large scale phylogenies without users effort. These updated phylogenies and their taxonomic labels can be easily linked to the Open Tree of Life project, which provides automated reporting of concordance and conflict between the updated tree and existing taxonomies and published phylogenies. Bring your own datasets and check it out!


1 - University of California, Merced, School of Natural Sciences, CA
2 - University of California, Merced, School of Natural Sciences

Keywords:
Phylogenetics
workflow
automatic updating.

Presentation Type: Workshop
Number:
Abstract ID:64
Candidate for Awards:None

Canceled

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