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ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
TLDR
This work has extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.
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Using consensus networks to visualize contradictory evidence for species phylogeny.
TLDR
This work compares gene trees for eight yeast genomes and shows that consensus networks have potential for helping to visualize contradictory evidence for species phylogenies.
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Delta plots: a tool for analyzing phylogenetic distance data.
TLDR
The method is shown to be capable of identifying single recombinant taxa on the basis of distance information alone, provided the parents of the recombinant sequence are sufficiently divergent and the mixture of tree histories is not strongly skewed toward a single tree.
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Reconstructing the evolutionary history of polyploids from multilabeled trees.
TLDR
This paper presents a general method for constructing phylogenetic networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties and discusses its use in reconstructing the evolutionary history of plant allopolyploids.
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Using supernetworks to distinguish hybridization from lineage-sorting
TLDR
Filtered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies.
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Basic Phylogenetic Combinatorics
TLDR
This book focuses on the interrelationship between the principal options for encoding phylogenetic trees: split systems, quartet systems and metrics, and highlights how each provides a unique perspective for viewing and perceiving the combinatorial structure of a phylogenetic tree.
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Spectronet: a package for computing spectra and median networks.
TLDR
Spectronet is a package that uses various methods for exploring and visualising complex evolutionary signals by computing a collection of weighted splits or bipartitions of the taxa and then allows the user to interactively analyse the resulting collection using tools such as Lento-plots and median networks.
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PADRE: a package for analyzing and displaying reticulate evolution
TLDR
The software package PADRE (Package for Analyzing and Displaying Reticulate Evolution) is described, allowing the reconstruction of complex evolutionary histories for polyploids in the form of phylogenetic networks.
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Orthology relations, symbolic ultrametrics, and cographs
TLDR
This work presents some new characterizations for symbolic ultrametrics and new algorithms for recovering the associated trees, with an emphasis on how these algorithms could be potentially extended to deal with arbitrary orthology relations.
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Inferring polyploid phylogenies from multiply-labeled gene trees
TLDR
A heuristic method for computing a consensus tree of multiply-labeled trees and illustrates the applicability of the method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels.
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