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OCTAL: Optimal Completion of gene trees in polynomial time

Overview of attention for article published in Algorithms for Molecular Biology, March 2018
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  • Above-average Attention Score compared to outputs of the same age (56th percentile)

Mentioned by

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7 tweeters

Citations

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3 Dimensions

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4 Mendeley
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Title
OCTAL: Optimal Completion of gene trees in polynomial time
Published in
Algorithms for Molecular Biology, March 2018
DOI 10.1186/s13015-018-0124-5
Pubmed ID
Authors

Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy Warnow

Abstract

For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain all of the species of interest. As incomplete gene trees can impact downstream analyses, accurate completion of gene trees is desirable. We introduce theOptimal Tree Completion problem, a general optimization problem that involves completing an unrooted binary tree (i.e., adding missing leaves) so as to minimize its distance from a reference tree on a superset of the leaves. We presentOCTAL, an algorithm that finds an optimal solution to this problem when the distance between trees is defined using the Robinson-Foulds (RF) distance, and we prove that OCTAL runs in [Formula: see text] time, wherenis the total number of species. We report on a simulation study in which gene trees can differ from the species tree due to incomplete lineage sorting, and estimated gene trees are completed using OCTAL with a reference tree based on a species tree estimated from the multi-locus dataset. OCTAL produces completed gene trees that are closer to the true gene trees than an existing heuristic approach in ASTRAL-II, but the accuracy of a completed gene tree computed by OCTAL depends on how topologically similar the reference tree (typically an estimated species tree) is to the true gene tree. OCTAL is a useful technique for adding missing taxa to incomplete gene trees and provides good accuracy under a wide range of model conditions. However, results show that OCTAL's accuracy can be reduced when incomplete lineage sorting is high, as the reference tree can be far from the true gene tree. Hence, this study suggests that OCTAL would benefit from using other types of reference trees instead of species trees when there are large topological distances between true gene trees and species trees.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 4 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 4 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 2 50%
Professor 1 25%
Researcher 1 25%
Readers by discipline Count As %
Unspecified 1 25%
Biochemistry, Genetics and Molecular Biology 1 25%
Computer Science 1 25%
Agricultural and Biological Sciences 1 25%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 April 2018.
All research outputs
#7,118,563
of 13,793,900 outputs
Outputs from Algorithms for Molecular Biology
#75
of 208 outputs
Outputs of similar age
#133,597
of 317,618 outputs
Outputs of similar age from Algorithms for Molecular Biology
#1
of 1 outputs
Altmetric has tracked 13,793,900 research outputs across all sources so far. This one is in the 47th percentile – i.e., 47% of other outputs scored the same or lower than it.
So far Altmetric has tracked 208 research outputs from this source. They receive a mean Attention Score of 3.0. This one has gotten more attention than average, scoring higher than 61% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 317,618 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them