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
Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.
Sign Up to like & getrecommendations! Published in 2017 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2017.03.027
Abstract: While phylogenetic analysis of transcriptomes of the same tissue is usually congruent with the species tree, the controversy emerges when multiple tissues are included, that is, whether species from the same tissue are clustered together,… read more here.
Keywords: transcriptome evolution; phylogenetic network; evolution; model transcriptome ... See more keywords
Reply to Sánchez-Pacheco et al., Chookajorn, and Mavian et al.: Explaining phylogenetic network analysis of SARS-CoV-2 genomes
Sign Up to like & getrecommendations! Published in 2020 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2007433117
Abstract: We calculated a phylogenetic analysis network of the 160 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complete genomes submitted to the international Global Initiative on Sharing Avian Influenza Data (GISAID) database by early March 2020,… read more here.
Keywords: network; analysis; phylogenetic network; coronavirus ... 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
Improved Fixed-parameter Algorithm for the Tree Containment Problem on Unrooted Phylogenetic Network.
Sign Up to like & getrecommendations! Published in 2021 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2021.3111660
Abstract: Phylogenetic trees are unable to represent the evolutionary process for a collection of species if reticulation events happened, and a generalized model named phylogenetic network was introduced consequently. However, the representation of the evolutionary process… read more here.
Keywords: parameter algorithm; problem; fixed parameter; phylogenetic network ... See more keywords
Defining Phylogenetic Network Distances Using Cherry Operations.
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2022.3162991
Abstract: In phylogenetic networks, picking a cherry consists of removing a leaf that shares a parent with another leaf, or removing a reticulate edge whose endpoints are parents of leaves. Cherry-picking operations were recently shown to… read more here.
Keywords: network; distances using; network distances; cherry picking ... See more keywords