As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).
In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.
During my M.Sc. thesis I started to use the Bayesian phylogenetic MrBayes on clusters that do not make it feasible to keep open a terminal window. This meant I had to use ‘batch mode’, meaning I could only follow the status of the MrBayes run through the log files.