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ASTRID: Accurate Species TRees from Internode Distances

Pranjal Vachaspati, Tandy Warnow
doi: https://doi.org/10.1101/023036
Pranjal Vachaspati
1Department of Computer Science, University of Illinois at Urbana-Champaign, 201 N. Goodwin Avenue, Urbana, IL, 61801 USA
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Tandy Warnow
1Department of Computer Science, University of Illinois at Urbana-Champaign, 201 N. Goodwin Avenue, Urbana, IL, 61801 USA
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  • For correspondence: warnow@illinois.edu
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Abstract

Background Incomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets.

Results We have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours.

Conclusions ASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 22, 2015.
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ASTRID: Accurate Species TRees from Internode Distances
Pranjal Vachaspati, Tandy Warnow
bioRxiv 023036; doi: https://doi.org/10.1101/023036
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ASTRID: Accurate Species TRees from Internode Distances
Pranjal Vachaspati, Tandy Warnow
bioRxiv 023036; doi: https://doi.org/10.1101/023036

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