MASH and khmer abundance

The other day at PHE we were investigating use of MASH sketches to find closest isolates. If you don’t already know about MASH, it’s a MinHash algorithm implemented by Adam Phillippy’s group (@aphillippy). It is fast and pretty neat, but the resulting distance is directly related to the errors in the sequencing. On one hand,…

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…