pyseerpyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population on a phenotype of interest, while accounting for potentially very strong confounding population structure. This allows for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses.
For more information visit the pyseer website.
These versions of pyseer are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.