ulakes
Population genetics of cichlid fish in lakes Victoria, Kivu and Mweru
This is the code repository for our paper, Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations by Matt McGee, Russell Neches and Ole Seehausen, manuscript ID MEC-15-0615.R2.
In addition to many of the key intermediate data files, we have included the following pieces of code and data required to reproduce our results.
Notebooks
These notebooks are build using Jupyter Notebook 4.0.6 (a.k.a., iPython notebook)
CichlidVariantCalling.ipynb
: Read alignment and variant callingulakes.ipynb
: Basic population geneticsStatsAndFigures.ipynb
: Statistics and figures
Data
threepairs_mitogenome_tree.nex
: Phylogenetic tree of mitochondrial genomesthreepairs_mitogenomes.fst
: Mitochondria genome sequences