Plotting trees with plotTree

Kat Holt’s lab have a nice set of scripts that wrap around ete2 which makes it nice ‘n’ easy to annotate trees – plotTree! It works out the box! They have some great installation and usage instructions on the github, and some examples for the R half of the code, but the examples for the python bit are…

My time at PHE in numbers

I’m leaving PHE today, and thought I would try and reflect on my time spent here, and one way of doing that is to put some numbers on things. None of the below should be taken as an official PHE statistic 🙂 Number of years – 8 Number of organisational names – 2 Number of…

how to do age-sex pyramid in excel

Say you have an age-sex breakdown and you want to summarise it in the usual way (as below). how do you do this in excel? this is definitely a post from the annals of ‘so ridiculous i had to write it down’. So, you have to give one of your sexes minus values, and then…

how to give a talk

I’m at IMMEM 2016 and there have been some great talks. However, some of them have been hampered by delivery, so i thought i would write a quick post on some things i try to do (a lot stolen from matt might and jen gardy). I used to have a job selling windows (made of…

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…