Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics.
Ecography, 2016 During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology.
Florent Mazel +6 more
semanticscholar +1 more source
How can Sequence Alignment Method Affect the Phylogenetic Relationship Results?
Scientific Papers Animal Science and Biotechnologies, 2023 Sequence alignment is a fundamental step before analysing the phylogenetic relationships between organisms. The effect of the alignment method on the phylogenetic relationship results has not been well studied.
Hossam F. Abou-Shaara
doaj
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
BMC Bioinformatics, 2009 Background To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise.
Pontarotti Pierre +2 more
doaj +1 more source
A Metric on Phylogenetic Tree Shapes
bioRxiv, 2016 The shapes of evolutionary trees are influenced by the nature of the evolutionary process, but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape.
C. Colijn, G. Plazzotta
semanticscholar +1 more source
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
PLoS ONE, 2017 Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications.
U. Mai, Erfan Sayyari, S. Mirarab
semanticscholar +1 more source
Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses
Genome Biology and Evolution, 2016 Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods.
R. Lanfear, Xia Hua, D. Warren
semanticscholar +1 more source
Phylogenetic search through partial tree mixing
BMC Bioinformatics, 2012 Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of ...
Sundberg Kenneth +5 more
doaj +1 more source
Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes.
PLoS ONE, 2015 Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence.
Elizabeth E Boyle, Sarah J Adamowicz
doaj +1 more source
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
Human Mutation, 2009 Human mitochondrial DNA is widely used as tool in many fields including evolutionary anthropology and population history, medical genetics, genetic genealogy, and forensic science.
M. van Oven, M. Kayser
semanticscholar +1 more source
TreeView: an application to display phylogenetic trees on personal computers
Comput. Appl. Biosci., 1996 TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists.
R. Page
semanticscholar +1 more source