Results 11 to 20 of about 7,231,771 (330)
STRIDE: Species Tree Root Inference from Gene Duplication Events. [PDF]
Mol Biol Evol, 2017 The correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. We present STRIDE, a
Emms DM, Kelly S.
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ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony [PDF]
Bioinformatics, 2016 Abstract Summary: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation ...
E. Jacox +4 more
semanticscholar +5 more sources
Neighbourhood interactions drive overyielding in mixed-species tree communities. [PDF]
Nat Commun, 2018 Theory suggests that plant interactions at the neighbourhood scale play a fundamental role in regulating biodiversity–productivity relationships (BPRs) in tree communities.
Fichtner A +5 more
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The performance of coalescent-based species tree estimation methods under models of missing data. [PDF]
BMC Genomics, 2018 Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny.
Nute M, Chou J, Molloy EK, Warnow T.
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SPECIES TREE INFERENCE FROM GENOMIC SEQUENCES USING THE LOG-DET DISTANCE. [PDF]
SIAM J Appl Algebr Geom, 2019 The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution.
Allman ES, Long C, Rhodes JA.
europepmc +3 more sources
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. [PDF]
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.
Mai U, Sayyari E, Mirarab S.
europepmc +2 more sources
Journal of Forest Science, 2023 In 2021, measurements were done at two international provenance research trials for silver fir originating from the same series of experiments. The investigation was carried out in the location Vítkov and Úsov, where both trials were established ...
Martin Fulín +3 more
doaj +1 more source
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees
Bioinform., 2022 MOTIVATION Species tree inference from multi-copy gene trees has long been a challenge in phylogenomics. The recent method ASTRAL-Pro has made large strides by enabling multi-copy gene family trees as input and has been quickly adopted.
Chao Zhang, S. Mirarab
semanticscholar +1 more source
bioRxiv, 2021 Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees.
Benoit Morel +5 more
semanticscholar +1 more source
wQFM: highly accurate genome-scale species tree estimation from weighted quartets
Bioinform., 2021 MOTIVATION Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles ...
Mahim Mahbub +4 more
semanticscholar +1 more source