Consequences of substitution model selection on protein ancestral sequence reconstruction
The selection of the best-fitting substitution model of molecular evolution is a traditional step
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
Substitution models of protein evolution with selection on enzymatic activity
Substitution models of evolution are necessary for diverse evolutionary analyses including
phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical …
phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical …
[HTML][HTML] Influence of substitution model selection on protein phylogenetic tree reconstruction
Probabilistic phylogenetic tree reconstruction is traditionally performed under a best-fitting
substitution model of molecular evolution previously selected according to diverse statistical …
substitution model of molecular evolution previously selected according to diverse statistical …
The evolution of the HIV-1 protease folding stability
The evolution of structural proteins is generally constrained by the folding stability. However,
little is known about the particular capacity of viral proteins to accommodate mutations that …
little is known about the particular capacity of viral proteins to accommodate mutations that …
Data-specific substitution models improve protein-based phylogenetics
Calculating amino-acid substitution models that are specific for individual protein data sets is
often difficult due to the computational burden of estimating large numbers of rate …
often difficult due to the computational burden of estimating large numbers of rate …
The structure of evolutionary model space for proteins across the tree of life
GE Scolaro, EL Braun - Biology, 2023 - mdpi.com
Simple Summary The relative rates of amino acid substitution over evolutionary time reflect
the chemical properties of amino acids. Substitutions that result in an amino acid similar to …
the chemical properties of amino acids. Substitutions that result in an amino acid similar to …