MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping
RC Edgar - BioRxiv, 2021 - biorxiv.org
Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA)
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …
Six impossible things before breakfast: assumptions, models, and belief in molecular dating
L Bromham - Trends in Ecology & Evolution, 2019 - cell.com
Confidence in molecular dating analyses has grown with the increasing sophistication of the
methods. Some problematic cases where molecular dates disagreed with paleontological …
methods. Some problematic cases where molecular dates disagreed with paleontological …
Identifying clusters of high confidence homologies in multiple sequence alignments
Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are
usually taken to be a known and fixed quantity on which to perform downstream analysis …
usually taken to be a known and fixed quantity on which to perform downstream analysis …
Alignment modulates ancestral sequence reconstruction accuracy
Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying
ancient proteins and comparing biochemical properties between parental or extinct species …
ancient proteins and comparing biochemical properties between parental or extinct species …
A genome-scale investigation of how sequence, function, and tree-based gene properties influence phylogenetic inference
Molecular phylogenetic inference is inherently dependent on choices in both methodology
and data. Many insightful studies have shown how choices in methodology, such as the …
and data. Many insightful studies have shown how choices in methodology, such as the …
PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score
U Bastolla, D Abia, O Piette - Bioinformatics, 2023 - academic.oup.com
Motivation Evolutionary inference depends crucially on the quality of multiple sequence
alignments (MSA), which is problematic for distantly related proteins. Since protein structure …
alignments (MSA), which is problematic for distantly related proteins. Since protein structure …
Multiple sequence alignment averaging improves phylogeny reconstruction
The classic methodology of inferring a phylogenetic tree from sequence data is composed of
two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is …
two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is …
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and
to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive …
to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive …
Intraspecies variation of the mitochondrial genome: An evaluation for phylogenetic approaches based on the conventional choices of genes and segments on …
Intraspecies nucleotide sequence variation is a key to understanding the evolutionary
history of a species, such as the geographic distribution and population structure. To date …
history of a species, such as the geographic distribution and population structure. To date …
[HTML][HTML] Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)
Phylogenetic studies have resolved most relationships among Eutherian Orders. However,
the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows …
the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows …