Phylogenetic tree and variable gene content inference
Phylogenetic species tree inference from gene trees despite paralogy
... Tagging The tagNJ A−pro technique can lower the rRFD even though many distances between gene tree leaves are not considered for the overall distance calculation at all. Therefore, we will also evaluate ...
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Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
... so-called gene trees by contrast with the species tree that contains them (Maddison ...logenetic tree with tips annotated by phenotypes gives a first impression of their relationship, and this type of ...
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Gene tree correction for reconciliation and species tree inference
... Keywords: Gene tree, Species tree, Reconciliation, Error correction, Maximum agreement subtree (MAST) Background Almost all genomes which have been studied contain genes that are present in two or ...
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Reversible polymorphism aware phylogenetic models and their application to tree inference
... of gene fl ow. However, we want to assess robustness against gene fl ow in the ...the tree, ...direct inference of effective population size as well as germline mutation ...
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Untangling the tree of life: Which partitioning strategies improve phylogenetic inference?
... The leading principle of Bayesian analysis is the separation of prior beliefs from evidence, so a prior should be in no way influenced by the data. Some of the parti- tioning strategies tested here violate this paradigm ...
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Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer
... matR tree closely matched results from other molecular phylo- genetic investigations of ...mitochondrial gene, nad1, has been reported for Rafflesia and Sapria, both of which occur on the same clade as ...
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CiteSeerX — Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow
... Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial ...cause gene tree discordance and ...
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CiteSeerX — Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow
... Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial ...cause gene tree discordance and ...
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Combining tree-based and dynamical systems for the inference of gene regulatory networks
... network inference problem, called ...of gene expression, the on/off model of gene expression ( Ocone et ...non-parametric, tree-based method modelled on the state-of-the-art GENIE3 method ( ...
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CiteSeerX — A rticle Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow
... Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial ...cause gene tree discordance and ...
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MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
... the inference of trees, transfers and ...and gene tree reconstructions to explain part of the ...associated gene tree, the definition of the time constraint could be relaxed to the ...
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OrthoFinder: phylogenetic orthology inference for comparative genomics
... from gene trees that also vary in terms of scal- ability and accuracy ...the inference of a complete set of rooted gene trees from a set of species proteomes would be a complex, multi-step process ...
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
... on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic ...
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Statistical analysis of species tree inference
... particular gene from several species, a phylogenetic gene tree can be inferred using the classical computational methods for constructing ...individual gene trees does not always match ...
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Building a phylogenetic tree
... Introduction Modern taxonomy tries to classify organisms according to their relatedness. Earlier taxonomic systems used morphological or anatomical similarities that did not al- ways reflect true evolutionary ...
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ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
... and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align ...single phylogenetic tree that can be used for diversity ...foundation tree ...
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Polytomies and bayesian phylogenetic inference
... focal tree topology has been sampled up to iteration ...focal tree topology was sampled; the MCMC estimate of the posterior prob- ability of the focal tree topology is thus T N /N ...
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How to Read a Phylogenetic Tree
... a phylogenetic tree, you will see that all of the branches have at least one, and more likely many, characters on them (the slash marks on ...a tree because it’s visually ...the tree showing ...
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Phylogenetic diversity of Amazonian tree communities
... greatest phylogenetic diversity been accumulated in communities overlaying old geological formations? Communities on old geological substrates in the Brazilian and Guianan Shields showed lower PDss than ...
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Displaying Phylogenetic Tree with 3D Clustering
... the phylogenetic tree corresponds to a point in the 3D dimension reduction ...with phylogenetic trees, one way to do that is to display the clusters of sequences on one side, then the ...
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