Notes about ClonalFrameML

Here are my notes of the article about ClonalFrameML, a program that detects recombined regions in a multi-sequence alignment, infers phylogenetic relationships when correcting for recombination, reconstructs ancestral state, and imputes SNPs under a maximum-likelihood (ML) framework.

To tree or not to tree: an introduction of phylogenetic networks

Phylogenetic reconstruction is of crucial importance to elucidate bacterial population structure, epidemiology and evolutionary histories. By far phylogenetic networks and trees are the most common approaches used for studying the evolutionary history of a bacterial population. However, concepts and methodology underlying phylogenetic reconstruction can be challenging to beginners. As such, I share my notes on relevant literature in this post to address these obstacles. In particular, I compare different kinds of phylogenetic networks to show their pros and cons under various conditions.

Population structure, phylogenetic signal, recombination vs. mutations

Recently, I reviewed several concepts about recombination and mutation in bacterial genomes when I was revising my manuscript of GeneMates. In this post, I summarise my understandings to two groups of terms and two measures (r/m and ρ/θ) that are relevant to these biological events, and tabulate values of these measures in six bacterial species.