Literature DB >> 18474508

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

André Wehe1, Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein.   

Abstract

UNLABELLED: DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. AVAILABILITY: DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Entities:  

Mesh：

Year:  2008        PMID： 18474508     DOI： 10.1093/bioinformatics/btn230

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  55 in total

1.  Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.

Authors:  Laura A Katz; Jessica R Grant; Laura Wegener Parfrey; J Gordon Burleigh
Journal:  Syst Biol       Date:  2012-02-14       Impact factor: 15.683

2.  Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom.

Authors:  Edgar M Medina; Gary W Jones; David A Fitzpatrick
Journal:  J Mol Evol       Date:  2011-09-22       Impact factor: 2.395

3.  The genome of melon (Cucumis melo L.).

Authors:  Jordi Garcia-Mas; Andrej Benjak; Walter Sanseverino; Michael Bourgeois; Gisela Mir; Víctor M González; Elizabeth Hénaff; Francisco Câmara; Luca Cozzuto; Ernesto Lowy; Tyler Alioto; Salvador Capella-Gutiérrez; Jose Blanca; Joaquín Cañizares; Pello Ziarsolo; Daniel Gonzalez-Ibeas; Luis Rodríguez-Moreno; Marcus Droege; Lei Du; Miguel Alvarez-Tejado; Belen Lorente-Galdos; Marta Melé; Luming Yang; Yiqun Weng; Arcadi Navarro; Tomas Marques-Bonet; Miguel A Aranda; Fernando Nuez; Belén Picó; Toni Gabaldón; Guglielmo Roma; Roderic Guigó; Josep M Casacuberta; Pere Arús; Pere Puigdomènech
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-02       Impact factor: 11.205

4.  Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.

Authors:  Laura Wegener Parfrey; Jessica Grant; Yonas I Tekle; Erica Lasek-Nesselquist; Hilary G Morrison; Mitchell L Sogin; David J Patterson; Laura A Katz
Journal:  Syst Biol       Date:  2010-07-23       Impact factor: 15.683

5.  Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Authors:  J Gordon Burleigh; Mukul S Bansal; Oliver Eulenstein; Stefanie Hartmann; André Wehe; Todd J Vision
Journal:  Syst Biol       Date:  2010-12-24       Impact factor: 15.683

6.  Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods.

Authors:  Dayana E Salas-Leiva; Alan W Meerow; Michael Calonje; M Patrick Griffith; Javier Francisco-Ortega; Kyoko Nakamura; Dennis W Stevenson; Carl E Lewis; Sandra Namoff
Journal:  Ann Bot       Date:  2013-08-29       Impact factor: 4.357

7.  DrML: probabilistic modeling of gene duplications.

Authors:  Paweł Górecki; Oliver Eulenstein
Journal:  J Comput Biol       Date:  2013-09-27       Impact factor: 1.479

8.  Are the duplication cost and Robinson-Foulds distance equivalent?

Authors:  Yu Zheng; Louxin Zhang
Journal:  J Comput Biol       Date:  2014-07-02       Impact factor: 1.479

9.  Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm.

Authors:  Thérèse A Holton; Davide Pisani
Journal:  Genome Biol Evol       Date:  2010-07-12       Impact factor: 3.416

10.  Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.

Authors:  Cécile Ané
Journal:  Genome Biol Evol       Date:  2011-02-28       Impact factor: 3.416
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.