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The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees
Results from phylogenetic analyses that study the evolution of species according to their biological characteristics are frequently structured as...
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Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression
Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at...
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The TrEase web service: inferring phylogenetic trees with ease
Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use phylogeny as a tool to infer...
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Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples
Phylogenetic trees are a powerful means to display the evolutionary history of species, pathogens and, more recently, individual cells of the human...
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Phylogenetic Trees and Molecular Evolution A Hands-on Introduction with Uncertainty Quantification Corrected
This book serves as a brief introduction to phylogenetic trees and molecular evolution for biologists and biology students. It does so by presenting...
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Building trees by juggling information and following rules: an expert interview study on tree-building and phylogenetic inference
Tree-thinking is a fundamental skill set for understanding evolutionary theory and, thus, part of biological and scientific literacy. Research on...
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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional...
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Estimating Phylogenetic Trees
The third chapter covers a probability model of molecular evolution in a way designed to engage the readers with little interest in mathematics. That...
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NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the...
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vSNP: a SNP pipeline for the generation of transparent SNP matrices and phylogenetic trees from whole genome sequencing data sets
BackgroundSeveral single nucleotide polymorphism (SNP) pipelines exist, each offering its own advantages. Among them and described here is vSNP that...
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Complete chloroplast genomes of three copal trees (Bursera: Bullockia): comparative analysis and phylogenetic relationships
BackgroundBursera trees are conspicuous elements of the tropical dry forests in the Neotropics that have significant cultural value due to their...
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Local-scale soil nematode diversity in a subtropical forest depends on the phylogenetic and functional diversity of neighbor trees
PurposeUnderstanding the impact of neighbor tree diversity on soil biodiversity at the individual tree scale and clarifying which facets of neighbor...
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PhyloMissForest: a random forest framework to construct phylogenetic trees with missing data
BackgroundIn the pursuit of a better understanding of biodiversity, evolutionary biologists rely on the study of phylogenetic relationships to...
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Unveiling the impacts of forest loss on taxonomic and phylogenetic beta diversity of juvenile and adult tropical trees
Changes caused by anthropogenic disturbances are a major driver of local diversity, but their effects on the species replacement across space...
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Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split
BackgroundWe tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a...
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Embedding gene trees into phylogenetic networks by conflict resolution algorithms
BackgroundPhylogenetic networks are mathematical models of evolutionary processes involving reticulate events such as hybridization, recombination,...
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Introduction to Phylogenetic Trees
This chapter starts slow, without assuming more than a basic knowledge of biology or mathematics. Readers are exposed to the main concepts of the...
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Introduction to Phylogenetic Analysis of Molecular Sequence Data
Phylogeny is a model of the relationships between organisms, genes, proteins, or other structures based on common ancestry. It is also used for...
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Constructing phylogenetic networks via cherry picking and machine learning
BackgroundCombining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in...
