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#NEXUS
Begin data;
Dimensions ntax=3 nchar=500000;
Format datatype=dna symbols="ACTG" missing=? gap=-;
Matrix

H TCGCTGTCTCATACTATATGGAGAGTCAAGGGGGTTGAGATAATTGTCGCATTGTCTAAGTGAATGGCGTAAAGCGAAC.......
C CCGCTGTCTCATACTATATGGAGAGTCAAGGGGGTTGAGATAATTGTCGCATTGTCTAAGTGTATGGCGTAAAGCGAAC.......
G TCGCTGTCTCATACTATATGGAGAGTCAAGTGGGTTGAGATAATTGTCGCATTGTCTAAGTGAATGGCGTAAAGCGAAC.......
;End;

BEGIN TREES;
Tree t0 = ((H:150000,C:150000):150000, G:300000);
END;

BEGIN PHYLONET;
VI_coalHMM -bl -st (t0) -mu 2.5e-8 -rho 1.5e-8 -r 1000 -nb 2 -psp 50000 -nhsigma 20000 -pssigma 10000 -n0 10000 -ns 50 -niter 200 -nhmeanlr 20000 -psmeanlr 10000 -nhsigmalr 500 -pssigmalr 500 -nhsigmamin 10000 -pssigmamin 3000;
END;

 

This command will run VI_coalHMM for the data given. It will infer branch lengths of one leaf branch and one internal branchthe divergence times of HC ancestor and HCG ancestor, as well as the population sizes of HC ancestor and HCG ancestor. The starting tree is ((H:150000,C:150000):150000, G:300000);. That is, we start the search with HC ancestor divergence time of 150,000 generations and HCG ancestor divergence time of 300,000 generations (150,000 generations for both branch lengths). Note that the Newick string must be given in the TREES section and referenced in the PHYLONET section. The mutation rate is set to 2.5e-8 mutations per site per generation. The recombination rate is set to 1.5e-8 recombinations per site per generation. The cross-over rate -r is set to 1000 and the number of sub-branches -nb is set to 2. For details of -r and -nb see our paper. All other parameters are set as default.

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