Literature DB >> 18428792

Maximum-likelihood analysis using TREE-PUZZLE.

Heiko A Schmidt1, Arndt von Haeseler.   

Abstract

TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests.

Mesh：

Year:  2007        PMID： 18428792     DOI： 10.1002/0471250953.bi0606s17

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  23 in total

1.  Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions.

Authors:  Bruce S Seal; Derrick E Fouts; Mustafa Simmons; Johnna K Garrish; Robin L Kuntz; Rebekah Woolsey; Kathleen M Schegg; Andrew M Kropinski; Hans-W Ackermann; Gregory R Siragusa
Journal:  Arch Virol       Date:  2010-10-21       Impact factor: 2.574

2.  Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche.

Authors:  Janaki Purushe; Derrick E Fouts; Mark Morrison; Bryan A White; Roderick I Mackie; Pedro M Coutinho; Bernard Henrissat; Karen E Nelson
Journal:  Microb Ecol       Date:  2010-06-29       Impact factor: 4.552

3.  Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response.

Authors:  Kyle A Gurley; Sarah A Elliott; Oleg Simakov; Heiko A Schmidt; Thomas W Holstein; Alejandro Sánchez Alvarado
Journal:  Dev Biol       Date:  2010-08-10       Impact factor: 3.582

4.  A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals.

Authors:  Mary J O'Connell; Noeleen B Loughran; Thomas A Walsh; Mark T A Donoghue; Karl J Schmid; Charles Spillane
Journal:  Mamm Genome       Date:  2010-10-08       Impact factor: 2.957

5.  Evolution of diterpene metabolism: Sitka spruce CYP720B4 catalyzes multiple oxidations in resin acid biosynthesis of conifer defense against insects.

Authors:  Björn Hamberger; Toshiyuki Ohnishi; Britta Hamberger; Armand Séguin; Jörg Bohlmann
Journal:  Plant Physiol       Date:  2011-10-12       Impact factor: 8.340

6.  Downregulation of the T-cell receptor by human immunodeficiency virus type 2 Nef does not protect against disease progression.

Authors:  Jérôme Feldmann; Aleksandra Leligdowicz; Assan Jaye; Tao Dong; Hilton Whittle; Sarah L Rowland-Jones
Journal:  J Virol       Date:  2009-10-07       Impact factor: 5.103

7.  Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication.

Authors:  Andrew J Heidel; Hajara M Lawal; Marius Felder; Christina Schilde; Nicholas R Helps; Budi Tunggal; Francisco Rivero; Uwe John; Michael Schleicher; Ludwig Eichinger; Matthias Platzer; Angelika A Noegel; Pauline Schaap; Gernot Glöckner
Journal:  Genome Res       Date:  2011-07-14       Impact factor: 9.043

8.  Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.

Authors:  Zhemin Zhou; Xiaomin Li; Bin Liu; Lothar Beutin; Jianguo Xu; Yan Ren; Lu Feng; Ruiting Lan; Peter R Reeves; Lei Wang
Journal:  PLoS One       Date:  2010-01-14       Impact factor: 3.240

9.  Genomic Epidemiology of SARS-CoV-2 From Mainland China With Newly Obtained Genomes From Henan Province.

Authors:  Ning Song; Guang-Lin Cui; Qing-Lei Zeng
Journal:  Front Microbiol       Date:  2021-05-20       Impact factor: 5.640

10.  A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data.

Authors:  Catherine D Carrillo; Peter Kruczkiewicz; Steven Mutschall; Andrei Tudor; Clifford Clark; Eduardo N Taboada
Journal:  Front Cell Infect Microbiol       Date:  2012-05-01       Impact factor: 5.293
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