Preparing a tree file for use with path-o-gen

Path-o-gen is a handy tool from Andy Rambaut’s group ‘for investigating the temporal signal and ‘clocklikeness’ of molecular phylogenies’. It is a common pre-cursor to the more involved BEAST analysis, to see whether there is any clock-like signal (i.e. SNPs accumulating with time) in the phylogeny. I wanted to do this today to look at…

IQTree vs RAxML for phylogenetic tree construction

This is a guest post from Anthony Underwood. ——————– I’ve been exploring the use of IQ-TREE for rapid ML tree calculation. I’ve had reservations for a while when using RAxML since even with multi-threading it can take hours to run and have often instead submitted them to the CIPRES supercomputing facilities at phylo.org where the…

NCTC3000 PacBio MLST

TL;DR I have run Torsten’s MLST script on the NCTC PacBio genomes, here are the results. I’m a massive fan of the NCTC3000 project, a collaboration between the National Collection of Type Cultures and the Wellcome Trust, to PacBio sequence 3000 bacterial type strains from the NCTC collection. One of the reasons I like the…

Weird SRA/ENA discrepancy

I’m trying to download some data from the Sequence Read Archive but it seems to be behaving quite unusually. Just writing a post to summarise this and see if anyone has seen it before. If I get an answer from the SRA helpdesk, I will post it in the comments/an edit. I’m interested in ERR024630, or…

Science is vital – are academics?

Ok, overly provocative title perhaps? My point is that, the milkman* doesn’t ask for £20 with the promise that he will deliver milk in 20 years time. The normal state of transactions is that, you pay for something, you get something in return. Not for one second am I saying that I don’t think academic…

Science is vital – to public health

tl;dr? Science is Vital! Write George Osbourne a postcard, telling him why you think science is vital. Write to your MP! Last night I went to the Science is Vital rally (Science: as vital as ever). I have to express my admiration for all the organisers and presenters, who I thought did a tremendous job…

GenomeTrakr meeting notes

Notes for GenomeTrakr 2015 meeting Context These notes were taken during the FDA GenomeTrakr Meeting held at the Omni Shoreham Hotel in Washington DC, USA from 23-24 September 2015. The notes are intended to be as objective as possible. Personal opinions or speculation are prefixed by the author’s initials below: Contributors to this document PA…