Scripts and analyses performed in Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species.
Please refer to paper for exact methods used to perform BEAST divergence dating analysis using mtDNA, including jModel test. GNP mtDNA consensus sequence was constructed using ANGSD. Please see mtdna_ML.sh script for command.
Scripts relevant to Y-chromosome analyses can be found in the ychrom folder.
Mapping and Variant Calling scripts can be found in their respective folders.
Scripts for both genotype-based D-statistics (POPSTAT) and read sampling method (ANGSD) can be found here. Details of f3 and f4 runs using AdmixTools can be found in the paper's Material and Methods. Should you require further clarification on set-up and running of f-statistics please contact: Ludovica Molinaro ([email protected]) and Luca Pagani ([email protected]).
Please see the paper's Material and Methods section for exact parameters used in PLINK and smartPCA.
Scripts for running TreeMix iteratively with different migration edges can be found in the treemix folder.
Snakemake for PSMC can be found in the psmc folder. The include.bed file referred to in the Snakemake is the whitelist file (i.e. regions you WANT included).
For details on how these methods were run, please refer to the paper's Material and Methods section. Should you require further clarification on set-up and running of these analyses please contact: Ludovica Molinaro ([email protected]) and Luca Pagani ([email protected]).