I had the pleasure of meeting with Philip Hugenholtz at the Australian Centre for Ecogenomics at the University of Queensland last week. Even the architecture of the centre is designed after phylogenetic trees! Of the many projects going on amongst the team of about 35 there, is the extensive effort in fixing the genome tree …
The idea for GenomePeek began two years ago when I was working with Karl Klose, Liz Dinsdale, and Rob Edwards to assemble a P. salmonis genome that was being particularly difficult, even though we had 9 gigabases of sequencing. To check whether it was a single isolated genome I pulled out all the 16S reads …
Paper of potential interest to the microBEnet crowd: Phylogenetics and the human microbiome. It is a preprint in ArXiv by Erick Matsen. It focuses on the human microbiome but discusses the history of methods for phylogenetic analysis of microbial communities and it is quite good. Thanks to Erick for posting this to arXiv so that people …