Dear Jose,

There should be no difficulty in defining a 9x9 matrix (by simply writing it down) in the batch language code. However you need to 'alias' 7 low-frequency states into 1, which, unfortunately is tedious to do in the current implementation (i.e. one needs to create a temporary dataset in memory which maps 7 states down to 1). I'll write a little example in a short while on how to do that (assuming the RNA alphabet).

Cheers,
Sergei

Dear Jose,

Here's a code example for you. You should be able to define the map you need to and after that - the model you need to.

Cheers,
Sergei

Code:

DataSet 	  ds	    = ReadDataFile  ("../DistributionPackages/data/StemRNA.nex");
DataSetFilter rna16filter = CreateFilter (ds,2);

stateMap = {16,1}; /* how to map the states down, from AA,AC,...UU to a smaller state
					  the example here maps all unpaired states down to 1 */

stateMap [0]  = 0; /* AA -> State 0 */
stateMap [1]  = 0; /* AC -> State 0 */
stateMap [2]  = 0; /* AG -> State 0 */
stateMap [3]  = 1; /* AU -> State 1 */
stateMap [4]  = 0; /* CA -> State 0 */
stateMap [5]  = 0; /* CC -> State 0 */
stateMap [6]  = 2; /* CG -> State 2 */
stateMap [7]  = 0; /* CU -> State 0 */
stateMap [8]  = 0; /* GA -> State 0 */
stateMap [9]  = 3; /* GC -> State 3 */
stateMap [10] = 0; /* GG -> State 0 */
stateMap [11] = 4; /* GU -> State 4 */
stateMap [12] = 5; /* UA -> State 5 */
stateMap [13] = 0; /* UC -> State 0 */
stateMap [14] = 6; /* UG -> State 6 */
stateMap [15] = 0; /* UU -> State 0 */

stateCount	   = 7; /* how many states are there */
characterRemap = "ABCDEFGHIJKLMNOP"; /* just a hack to remap the characters */

newFilterString = "";
newFilterString * 128;

indexVector = {1,16} ["_MATRIX_ELEMENT_COLUMN_"];
unitVector  = {1,16} ["1"];
GetDataInfo (uniqueMap,rna16filter);

/* this code will map all ambiguities to ? */

newFilterString * ("$BASESET:\""+characterRemap[0][stateCount]+"\"\n");
newFilterString * ("$TOKEN: \"X\"=\""+characterRemap[0][stateCount]+"\"\n");

for (seq  = 0; seq < rna16filter.species; seq = seq + 1)
{
	GetString (seqI,rna16filter,seq);
	newFilterString * (">" + seqI + "\n");
	for (site = 0 ; site < rna16filter.sites; site = site + 1)
	{
		GetDataInfo (siteInfo, rna16filter,seq,uniqueMap[site]);
		stateCount = (unitVector*siteInfo)[0];
		if (stateCount != 1)
		{
			newFilterString * "X";
		}
		else
		{
			newFilterString * characterRemap[stateMap[(indexVector*siteInfo)[0]]];
		}
	}
	newFilterString * "\n";
}

newFilterString * 0;

DataSet		  reducedRNA	 = ReadFromString (newFilterString);
DataSetFilter reducedRNAFilter = CreateFilter   (reducedRNA,1);