Its been a while, apologies for the lack of posting…I haven’t been doing much writing on my thesis, I’ve just been in the lab, trying to get some sequences for my plants and in some cases failing miserably. I’m at the stage where I’m having to alter the PCR protocols and primers in order to get something from the most intractable samples. Nonetheless I have some sequences to work with, so it’s not entirely miserable, I guess!
My supervisor’s funding dried up very rapidly so I have had to basically halve my intended sample set – it’s still enough to write a Masters, but it’s going to be difficult to publish straight from my thesis without doing some extra work expanding my data set, although my supervisor also just got an article accepted for PNAS so it’s possible that some funding may forthcoming from the University some time in the near future…
At the moment I’m running a whole lot of phylogenetic analyses on my sequences producing trees, and hopefully, estimating relative branch lengths for my ingroups. Unfortunately methodological constraints have prevented me from getting sister taxa as my ingroup, so I am not able to run robust Relative Rates Tests, and have to rely solely on the estimated parameters that come out of Maximum Likelihood phylograms. At the moment I don’t have PAUP* on my computer, for which I first need to get the Mac OS9 Classic environment which for some reason I don’t have automatically…so I’m using the PHYML plugin of Geneious, to run some preliminary ML analyses just to sort out topology. Geneious is quite an impressive programme with a whole bunch of bioinformatic and computational biology tools, developed by BioMatters, a commercial group from the University of Auckland. I would seriously suggest downloading a demo version if you don’t have one just have a play around. It has a Bayesian analysis plugin – MrBayes – but my poor laptop crashed while running it!
Anyway more to come later – I have to run and do some work!
Recent Peer Review