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 …
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and
comparative genomics studies. However, from the same set of sequences different MSAs …
comparative genomics studies. However, from the same set of sequences different MSAs …
[HTML][HTML] Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences
Abstract Background Multiple Sequence Alignments (MSAs) are the starting point of
molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can …
molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can …
Phylogenomics
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. The abundance of genomic data for …
account whole genomes or large fractions of genomes. The abundance of genomic data for …
[HTML][HTML] Divergence and adaptive evolution of the gibberellin oxidase genes in plants
Y Huang, X Wang, S Ge, GY Rao - BMC Evolutionary Biology, 2015 - Springer
Background The important phytohormone gibberellins (GAs) play key roles in various
developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis …
developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis …
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 …
Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets
The estimation of multiple sequence alignments of protein sequences is a basic step in
many bioinformatics pipelines, including protein structure prediction, protein family …
many bioinformatics pipelines, including protein structure prediction, protein family …
Insertion–Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure
Y Yang, MV Braga, MD Dean - Genome Biology and Evolution, 2024 - academic.oup.com
A fundamental goal in evolutionary biology and population genetics is to understand how
selection shapes the fate of new mutations. Here, we test the null hypothesis that insertion …
selection shapes the fate of new mutations. Here, we test the null hypothesis that insertion …
Evidence of statistical inconsistency of phylogenetic methods in the presence of multiple sequence alignment uncertainty
AS Md Mukarram Hossain… - Genome biology and …, 2015 - academic.oup.com
Evolutionary studies usually use a two-step process to investigate sequence data. Step one
estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods …
estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods …
Indel reliability in indel-based phylogenetic inference
It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred
at the same position in two independent evolutionary lineages, and thus, indel-based …
at the same position in two independent evolutionary lineages, and thus, indel-based …