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Abstract Detail

Biodiversity Informatics & Herbarium Digitization

Kandziora, Martha [1], McTavish, Emily Jane [2].

Physcraper: automatic updating of phylogenies.

The rate of DNA sequencing has outpaced the ability of researchers to analyze sequence data.
This means that many species are not included in any published phylogeny, despite available sequence data. There is an opportunity to provide active, automated extension of the tree of life with new inferences made directly from sequence data. We have developed a software pipeline, physcraper, to add these new sequences into existing trees. It is a tool that allows for flexible sampling across different ranks.
Physcraper automates the updating of phylogenetic relationships by adding new homologous sequences to the existing alignment and builds a starting tree including the new sequences. The tool can either retrieve sequences from Genbank or from a file containing unpublished sequences. The use of a starting tree decreases the time to calculate a new tree. Physcraper generates new, integrated, maximum likelihood estimates of species relationships, with minimal researcher time and effort. The advantage is that the method allows different sampling depth across different ranks which permits to build custom phylogenies with a scientific method to select sequences for the rank of interest. We will present the workflow in more detail and show the ability of the method to update phylogenies using different angiosperm lineages as an example.

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1 - University of California, Merced, School of Natural Sciences, CA
2 - UC Merced, Life and Environmental Sciences, 5200 North Lake Rd, Merced, CA, 95343, USA

automatic updating.

Presentation Type: Oral Paper
Session: BIHD1, Biodiversity Informatics & Herbarium Digitization
Location: Tucson I/Starr Pass
Date: Monday, July 29th, 2019
Time: 3:00 PM
Number: BIHD1007
Abstract ID:541
Candidate for Awards:None


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