Bounds for phylogenetic network space metrics
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Mathematical Biology"
DOI: 10.1007/s00285-017-1171-0
Abstract: Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every… read more here.
Keywords: space; network; phylogenetic trees; leaf set ... See more keywords
Fast Compatibility Testing for Rooted Phylogenetic Trees
Sign Up to like & getrecommendations! Published in 2017 at "Algorithmica"
DOI: 10.1007/s00453-017-0330-4
Abstract: We present a new graph-based approach to the following basic problem in phylogenetic tree construction. Let $$\mathcal {P}= \{T_1, \ldots , T_k\}$$P={T1,…,Tk} be a collection of rooted phylogenetic trees over various subsets of a set… read more here.
Keywords: rooted phylogenetic; compatibility; phylogenetic trees; testing rooted ... See more keywords
Dimensional Reduction for the General Markov Model on Phylogenetic Trees
Sign Up to like & getrecommendations! Published in 2017 at "Bulletin of Mathematical Biology"
DOI: 10.1007/s11538-017-0249-6
Abstract: We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces… read more here.
Keywords: markov model; phylogenetic trees; dimensional reduction; model ... See more keywords
Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events.
Sign Up to like & getrecommendations! Published in 2021 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2021.110788
Abstract: Two recent high profile studies have attempted to use edge (branch) length ratios from large sets of phylogenetic trees to determine the relative ages of genes of different origins in the evolution of eukaryotic cells.… read more here.
Keywords: length ratios; order; conditions distributions; phylogenetic trees ... See more keywords
Block alignment: New representation and comparison method to study evolution of genomes.
Sign Up to like & getrecommendations! Published in 2018 at "Genomics"
DOI: 10.1016/j.ygeno.2018.11.003
Abstract: Genomes are not random sequences because natural selection has injected information in biological sequences for billions of years. Inspired by this idea, we developed a simple method to compare genomes considering nucleotide counts in subsequences… read more here.
Keywords: block alignment; phylogenetic trees; method; alignment new ... See more keywords
A vectorial tree distance measure
Sign Up to like & getrecommendations! Published in 2022 at "Scientific Reports"
DOI: 10.1038/s41598-022-08360-4
Abstract: A vectorial distance measure for trees is presented. Given two trees, we define a Tree-Alignment (T-Alignment). We T-align the trees from their centers outwards, starting from the root-branches, to make the next level as similar… read more here.
Keywords: phylogenetic trees; vectorial tree; distance measure; distance ... See more keywords
Confidence Sets for Phylogenetic Trees
Sign Up to like & getrecommendations! Published in 2018 at "Journal of the American Statistical Association"
DOI: 10.1080/01621459.2017.1395342
Abstract: ABSTRACT Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology, and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates their analysis. While our mathematical,… read more here.
Keywords: phylogenetic trees; sets phylogenetic; confidence sets; space ... See more keywords
tidy tree: A New Layout for Phylogenetic Trees
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msac204
Abstract: Abstract Many layouts exist for visualizing phylogenetic trees, allowing to display the same information (evolutionary relationships) in different ways. For large phylogenies, the choice of the layout is a key element, because the printable area… read more here.
Keywords: tidy tree; layout phylogenetic; phylogenetic trees; new layout ... See more keywords
Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data.
Sign Up to like & getrecommendations! Published in 2020 at "Systematic biology"
DOI: 10.1093/sysbio/syaa031
Abstract: The evolutionary dynamics of complex ecological traits - including multistate representations of diet, habitat, and behavior - remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges… read more here.
Keywords: complex ecological; phylogenetic trees; model; multivariate count ... See more keywords
Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling.
Sign Up to like & getrecommendations! Published in 2021 at "Systematic biology"
DOI: 10.1093/sysbio/syab083
Abstract: Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to… read more here.
Keywords: macroevolutionary modelling; phylogenetic trees; diversification; time ... See more keywords
A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.
Sign Up to like & getrecommendations! Published in 2023 at "Genome research"
DOI: 10.1101/gr.277669.123
Abstract: The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is… read more here.
Keywords: phylogenetic trees; network; aligning lineage; phylogenetic networks ... See more keywords