Z Yang - Molecular biology and evolution, 2007 - academic.oup.com
Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to …
The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the …
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain. org. Here …
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a …
A Stamatakis, P Hoover, J Rougemont - Systematic biology, 2008 - academic.oup.com
Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …
SQ Le, O Gascuel - Molecular biology and evolution, 2008 - academic.oup.com
Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood …
H Shimodaira - Systematic biology, 2002 - academic.oup.com
An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce …
Population genetics occupies a central role in a number of important biological and social undertakings. It is fundamental to our understanding of evolutionary processes, of plant and …
Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position …