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 cups…

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…