From 8859f72969f967152ccd7adca998f3afe12f6555 Mon Sep 17 00:00:00 2001 From: arzwa Date: Mon, 12 Sep 2022 17:01:41 +0200 Subject: [PATCH] update README --- README.md | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index d3654a9..8f48b69 100644 --- a/README.md +++ b/README.md @@ -21,23 +21,24 @@ Whale.jl is a julia library for **joint inference of gene tree topologies and their reconciliations to a species tree**. Whale uses the **amalgamation** -method of Szollosi et al. (2014) to efficiently compute the marginal likelihood -of the gene family under a duplication-loss model of gene family evolution over -a distribution of tree topologies. Whale also implements a duplication-loss and -whole-genome duplication (DLWGD) model (Rabier et al. 2014, Zwaenepoel et al. -2019). The latter can be used for the inference of ancient whole-genome -duplications (WGDs) from gene trees while taking into account gene tree and -reconciliation uncertainty. +method of [Szollosi et al. (2014)](https://doi.org/10.1093/sysbio/syt054) +to efficiently compute the marginal likelihood of the gene family under a +duplication-loss model of gene family evolution over a distribution of tree +topologies. Whale also implements a duplication-loss and whole-genome +duplication (DLWGD) model (Rabier et al. 2014, Zwaenepoel et al. 2019). The +latter can be used for the inference of ancient whole-genome duplications +(WGDs) from gene trees while taking into account gene tree and reconciliation +uncertainty. More specifically, this library can be used to - Statistically assess hypothetical whole-genome duplication (WGD) events in a - species phylogeny. + species phylogeny using maximum likelihood estimation (MLE) or Bayesian + inference. - Infer lineage-specific gene duplication and loss rates for a species phylogeny. - Infer high-quality (reconciled) gene trees given a known species tree using - Bayesian gene tree reconciliation [cf. Szöllősi *et - al.*](https://academic.oup.com/sysbio/article/64/1/e42/1634124) + Bayesian gene tree reconciliation. - Conduct Bayesian orthology inference. - All of the above at once.