Phylogenetic tree-building

1996 ◽  
Vol 26 (6) ◽  
pp. 589-617 ◽  
Author(s):  
David A. Morrison
Keyword(s):  
Phylogenetic Tree ◽  
Tree Building

Phylogenetic Tree Building Methods

2009 ◽  
pp. 329-353 ◽  
Author(s):  
Manuel Gil ◽  
Gaston H. Gonnet
Keyword(s):  
Phylogenetic Tree ◽  
Tree Building ◽  
Building Methods

scholarly journals Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes

Genomics ◽  
2014 ◽  
Vol 104 (1) ◽  
pp. 1-7 ◽  
Author(s):  
William J. Faison ◽  
Alexandre Rostovtsev ◽  
Eduardo Castro-Nallar ◽  
Keith A. Crandall ◽  
Konstantin Chumakov ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Whole Genome ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide ◽  
Human Genomes ◽  
Tree Building ◽  
Building Methods

scholarly journals Phylogenetic tree building in the genomic age

2020 ◽  
Vol 21 (7) ◽  
pp. 428-444 ◽  
Author(s):  
Paschalia Kapli ◽  
Ziheng Yang ◽  
Maximilian J. Telford
Keyword(s):  
Phylogenetic Tree ◽  
Tree Building

Building and Using Phylogenies

2016 ◽  
Author(s):  
Marc W. Cadotte ◽  
T. Jonathan Davies
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Likelihood Methods ◽  
Object Type ◽  
Maximum Likelihood Methods ◽  
R Packages ◽  
Tree Building ◽  
Common Ancestors

This chapter explains how to build a phylogeny for a certain set of species. A phylogenetic tree is a representation of species interrelatedness and conveys information about which taxa share recent common ancestors, which evolutionary groups (clades) species belong to, and the distances (time, genetic, or character differences) separating species. The chapter first considers two R packages called ape and picante for use in analysis of the R phylogenetic object (referred to as a phylo object type), along with a few other packages, before discussing the steps in reconstructing phylogenetic relationships. It also evaluates some tree-building approaches that are easily implemented in R, including distance-based methods and maximum likelihood methods. Finally, it describes ways of finding and adapting available phylogenetic trees, together with tree scaling and rate smoothing.

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