ArticleMolecular biology and evolution2015
CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.Genome biology and evolution · 2026Review
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
- Rhometa: Population recombination rate estimation from metagenomic read datasets.PLoS genetics · 2023Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- From molecules to populations: appreciating and estimating recombination rate variation.Nature reviews. Genetics · 2020Review
- LDJump: Estimating variable recombination rates from population genetic data.Molecular ecology resources · 2019Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- Improved Versions of Common Estimators of the Recombination Rate.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.Journal of molecular evolution · 2015Article
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
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4 authors.
Funding
Abstract
The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.