skills/bioskills/bio-phylogenetics-divergence-dating/scripts/mcmctree_setup.py

• write_control_file · function · L14-L53 — def write_control_file(outpath, seqfile, treefile, outfile='mcmctree.out', ndata=1, usedata=2, clock=2, model=4, alpha=0.5, ncatg=4, cleandata=0, bdparas='1 1 0.1', rgene_gamma='2 20 1', sigma2_gamma='1 10 1', burnin=50000, sampfreq=50, nsample=20000, seed=-1)
• format_calibration · function · L56-L64 — def format_calibration(cal_type, *args)
• build_calibrated_tree · function · L67-L75 — def build_calibrated_tree(newick, calibrations)
• generate_prior_and_posterior_configs · function · L78-L92 — def generate_prior_and_posterior_configs(seqfile, treefile, outdir)