Dear Wayne,

SUPPORT_MATRIX_LIST is an associative array with indices 0..N-1 where N is the number of data partitions in the likelihood function which ReconstructAncestors was called on. To get the matrix for the first partition just use:

Code:

STORE_ROOT_SUPPORT		= 1;
DataSet ancestralStates = ReconstructAncestors (lf);
fprintf (stdout, SUPPORT_MATRIX_LIST); /* associative array */
statesFor1stPartition = SUPPORT_MATRIX_LIST[0];
/* an SxC matrix; S = number of sites; C is the number of characters in the alphabet (4 for nucleotides) */

 

HTH,
Sergei