Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis
Full genome data sets are currently being explored on a regular basis to infer phylogenetic
trees, but there are often discordances among the trees produced by different genes. An …
trees, but there are often discordances among the trees produced by different genes. An …
Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics
The systematics and speciation literature is rich with discussion relating to the potential for
gene tree/species tree discordance. Numerous mechanisms have been proposed to …
gene tree/species tree discordance. Numerous mechanisms have been proposed to …
Information geometry for phylogenetic trees
MK Garba, TMW Nye, J Lueg… - Journal of Mathematical …, 2021 - Springer
We propose a new space of phylogenetic trees which we call wald space. The motivation is
to develop a space suitable for statistical analysis of phylogenies, but with a geometry based …
to develop a space suitable for statistical analysis of phylogenies, but with a geometry based …
Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)
S Herrando-Moraira, JA Calleja, P Carnicero… - Molecular Phylogenetics …, 2018 - Elsevier
Target enrichment is a cost-effective sequencing technique that holds promise for
elucidating evolutionary relationships in fast-evolving lineages. However, potential biases …
elucidating evolutionary relationships in fast-evolving lineages. However, potential biases …
An algorithm for morphological phylogenetic analysis with inapplicable data
Morphological data play a key role in the inference of biological relationships and
evolutionary history and are essential for the interpretation of the fossil record. The …
evolutionary history and are essential for the interpretation of the fossil record. The …
Toward a theory of statistical tree-shape analysis
To develop statistical methods for shapes with a tree-structure, we construct a shape space
framework for tree-shapes and study metrics on the shape space. This shape space has …
framework for tree-shapes and study metrics on the shape space. This shape space has …
[HTML][HTML] The space of ultrametric phylogenetic trees
A Gavryushkin, AJ Drummond - Journal of theoretical biology, 2016 - Elsevier
The reliability of a phylogenetic inference method from genomic sequence data is ensured
by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic …
by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic …
Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees
Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic
analysis of gene sequences typically produces a collection of these trees, one for each gene …
analysis of gene sequences typically produces a collection of these trees, one for each gene …
The effects of subsampling gene trees on coalescent methods applied to ancient divergences
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic
inference. We sampled eight empirical studies of ancient lineages with diverse numbers of …
inference. We sampled eight empirical studies of ancient lineages with diverse numbers of …
[PDF][PDF] On a matching distance between rooted phylogenetic trees
D Bogdanowicz, K Giaro - International Journal of Applied …, 2013 - sciendo.com
The Robinson–Foulds (RF) distance is the most popular method of evaluating the
dissimilarity between phylogenetic trees. In this paper, we define and explore in detail …
dissimilarity between phylogenetic trees. In this paper, we define and explore in detail …