Ancestral sequence reconstruction with NDCH(2) - Tancata/phylo GitHub Wiki

ML

Do ML optimisation of two composition vectors (one for the root, one for everywhere else): p4 2comp_Pickle.py alignment tree

Do ancestral sequence reconstruction p4 tree_optTree.p4_tPickle alignment 2comp_reconstruct.py

Bayesian

Fit the NDCH2 model on a fixed, rooted tree. Give a run number (0, 1, 2...) for purposes of multiple runs and subsequent comparisons. p4 sNdch2.py alignment tree runNum

Sample from the root composition. Also calculates an estimated OGT after Zeldovich. p4 sPosteriorSamples.py alignment tree runNum