#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 -st (t0) -mu 2.5e-8 -rho 1.5e-8 -r 1000 -nb 2;
END;