How to do a Dendroscope tanglegram

Tanglegrams are a very cool way of visualising the difference between two trees. There is an implementation in Dendroscope that allows them to be made very easily, IF you know how (it isn’t covered very well in the documentation). This is how. This is definitely one of those, ‘write it down before I forget’ blogs.…

Plot maps with R

Another thing I have learned to do while at HSPH is to make maps with a nice sprinkling of visual sugar e.g. proportional point sizes, different colours, different shapes. This post will take you through that. Thanks to Amy¬†Wesolowski at HSPH for teaching me how to do this! The commands below can also be downloaded…

Annotating phylogenetic trees

Once your phylogenetic tree gets above 50-100 strains it can become a bit unwieldy to analyse. One nice way of getting around this is to annotate your tree with relevant info e.g. serotype, phage type, source, date, location etc. A while ago, Tim wrote a script to annotate NEXUS format trees for viewing in e.g.…

Assessment of assembly

We, like many people, are interested in optimal de novo genome assembly. When you assemble a genome you want the best possible representation of the ‘true’ genome. How can we obtain the best possible representation? In the past we have used VelvetOptimiser to do our assemblies. This assembles with a range of k-mers and returns…