Beginner's guide on the use of PAML to detect positive selection
S Álvarez-Carretero, P Kapli… - Molecular biology and …, 2023 - academic.oup.com
The CODEML program in the PAML package has been widely used to analyze protein-
coding gene sequences to estimate the synonymous and nonsynonymous rates (d S and d …
coding gene sequences to estimate the synonymous and nonsynonymous rates (d S and d …
Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli
Comparative analyses of natural and mutated sequences have been used to probe
mechanisms of gene expression, but small sample sizes may produce biased outcomes. We …
mechanisms of gene expression, but small sample sizes may produce biased outcomes. We …
[BOOK][B] Molecular evolution: a statistical approach
Z Yang - 2014 - books.google.com
Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …
few decades, due to rapid accumulation of genetic sequence data, improved computer …
Trends in substitution models of molecular evolution
M Arenas - Frontiers in genetics, 2015 - frontiersin.org
Substitution models of evolution describe the process of genetic variation through fixed
mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost …
mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost …
Mutation rates in plastid genomes: they are lower than you might think
DR Smith - Genome Biology and Evolution, 2015 - academic.oup.com
Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to
be greater than that of the mitochondrial genome. This assumption is based on early …
be greater than that of the mitochondrial genome. This assumption is based on early …
Means to optimize protein expression in transgenic plants
KK Ullrich, M Hiss, SA Rensing - Current opinion in biotechnology, 2015 - Elsevier
Highlights•Multifactorial study designs result in improved prediction power.•More focus
should be placed on directional targeting to cell compartments.•Previously neglected inside …
should be placed on directional targeting to cell compartments.•Previously neglected inside …
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC
WH Gharib, M Robinson-Rechavi - Molecular biology and …, 2013 - academic.oup.com
Positive selection is widely estimated from protein coding sequence alignments by the
nonsynonymous-to-synonymous ratio ω. Increasingly elaborate codon models are used in a …
nonsynonymous-to-synonymous ratio ω. Increasingly elaborate codon models are used in a …
Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic
The iconic mountains of the Pantepui biogeographical region host many early-diverging
endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient …
endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient …
Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae)
The genus Pipa is a species-poor clade of Neotropical frogs and one of the most bizarre-
looking due to many highly derived anatomical traits related to their fully aquatic lifestyle …
looking due to many highly derived anatomical traits related to their fully aquatic lifestyle …
New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species
S Gajbhiye, PK Patra, MK Yadav - Acta tropica, 2017 - Elsevier
Codon usage bias is due to the non-random usage of synonymous codons for coding amino
acids. The synonymous sites are under weak selection, and codon usage bias is maintained …
acids. The synonymous sites are under weak selection, and codon usage bias is maintained …