Literature DB >> 31095496

Topological Metrizations of Trees, and New Quartet Methods of Tree Inference.

John A Rhodes.   

Abstract

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here, the rooted triple and quartet metrizations are introduced, and applied to formulate novel methods of inferring large trees from rooted triple and quartet data. These methods lead to new statistically consistent procedures for inference of a species tree from gene trees under the multispecies coalescent model.

Entities:  

Mesh:

Year:  2020        PMID: 31095496      PMCID: PMC7650847          DOI: 10.1109/TCBB.2019.2917204

Source DB:  PubMed          Journal:  IEEE/ACM Trans Comput Biol Bioinform        ISSN: 1545-5963            Impact factor:   3.710


  27 in total

1.  Quartet-based phylogenetic inference: improvements and limits.

Authors:  V Ranwez; O Gascuel
Journal:  Mol Biol Evol       Date:  2001-06       Impact factor: 16.240

2.  Quartets MaxCut: a divide and conquer quartets algorithm.

Authors:  Sagi Snir; Satish Rao
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2010 Oct-Dec       Impact factor: 3.710

3.  Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages.

Authors:  Jesús Fernández-Sánchez; Marta Casanellas
Journal:  Syst Biol       Date:  2015-11-11       Impact factor: 15.683

4.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

Authors:  O Gascuel
Journal:  Mol Biol Evol       Date:  1997-07       Impact factor: 16.240

5.  Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites.

Authors:  Julia Chifman; Laura Kubatko
Journal:  J Theor Biol       Date:  2015-03-17       Impact factor: 2.691

6.  Quartet inference from SNP data under the coalescent model.

Authors:  Julia Chifman; Laura Kubatko
Journal:  Bioinformatics       Date:  2014-08-07       Impact factor: 6.937

7.  The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Authors:  N Saitou; M Nei
Journal:  Mol Biol Evol       Date:  1987-07       Impact factor: 16.240

8.  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Authors:  Siavash Mirarab; Tandy Warnow
Journal:  Bioinformatics       Date:  2015-06-15       Impact factor: 6.937

9.  ASTRID: Accurate Species TRees from Internode Distances.

Authors:  Pranjal Vachaspati; Tandy Warnow
Journal:  BMC Genomics       Date:  2015-10-02       Impact factor: 3.969

10.  The performance of coalescent-based species tree estimation methods under models of missing data.

Authors:  Michael Nute; Jed Chou; Erin K Molloy; Tandy Warnow
Journal:  BMC Genomics       Date:  2018-05-08       Impact factor: 3.969

View more
  6 in total

1.  MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R.

Authors:  John A Rhodes; Hector Baños; Jonathan D Mitchell; Elizabeth S Allman
Journal:  Bioinformatics       Date:  2021-07-19       Impact factor: 6.937

2.  Identifiability of species network topologies from genomic sequences using the logDet distance.

Authors:  Elizabeth S Allman; Hector Baños; John A Rhodes
Journal:  J Math Biol       Date:  2022-04-07       Impact factor: 2.164

3.  A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements.

Authors:  Gautam Dasarathy; Elchanan Mossel; Robert Nowak; Sebastien Roch
Journal:  J Math Biol       Date:  2022-04-08       Impact factor: 2.164

4.  Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance.

Authors:  Samaneh Yourdkhani; John A Rhodes
Journal:  Bull Math Biol       Date:  2020-07-16       Impact factor: 1.758

5.  Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.

Authors:  Elizabeth S Allman; Jonathan D Mitchell; John A Rhodes
Journal:  Syst Biol       Date:  2022-06-16       Impact factor: 9.160

6.  NANUQ: a method for inferring species networks from gene trees under the coalescent model.

Authors:  Elizabeth S Allman; Hector Baños; John A Rhodes
Journal:  Algorithms Mol Biol       Date:  2019-12-06       Impact factor: 1.405

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.