diff --git a/README.md b/README.md index e60ce0c..2637d22 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,6 @@ Models describing evolution at the codon level allow the estimation of measures of the selective forces acting on proteins ([Kosiol et. al. 2000](https://academic.oup.com/mbe/article-abstract/24/7/1464/986344)). - The available implementation is only M0 currently, also called as GY94, first published by [Goldman & Yang 1994](https://academic.oup.com/mbe/article-abstract/11/5/725/1008711), @@ -21,6 +20,10 @@ can be calculated as: The above two figures are copied from [Yang et al. 2000](http://www.genetics.org/content/155/1/431.short). +The model implementation in Java was ported from [BEAST 1](https://github.com/beast-dev/beast-mcmc) project. +The code was modified (including bug-fixing) to fit in [BEAST 2](https://github.com/CompEvol/beast2) +and also tested comparing with the [codeml](http://abacus.gene.ucl.ac.uk/software/paml.html) results. + ## Tutorial The tutorial is available in [wiki](https://github.com/BEAST2-Dev/codonmodels/wiki). @@ -59,7 +62,8 @@ The xml to use __M0__ looks like: ``` Note: the tree likelihood has to use the codon alignment not the nucleotide alignment. -``` + +```xml @@ -98,9 +102,9 @@ describing codon frequencies is increased. ## Citation -Dong Xie. (2017, November 1). Codon substitution models v1.0.0. Zenodo. +Dong Xie & Remco Bouckaert, (2018, April 12), Codon substitution models v1.1.0, Zenodo, http://doi.org/10.5281/zenodo.1039992 ## Note -This package is depending on BEAST 2.5.x, which will release on Match 2018. +This package is depending on BEAST 2.5.x.