Hi hanan,

1). Branch-site REL assumes that the alignment you feed it has no recombinants. You could screen the alignment to ensure that that's the case.
2). Internal node names are assigned automatically -- other than the tree ps file (which can sometimes be hard to read, I'll see if I can improve the output), BS-REL does not output node names.
There are several ways to get around this.

(a). You can name the nodes you care about in the tree string, e.g.

((a,b)ab,(c,d),e)

In this case the ancestor of a and b will not be given a default name, but rather the name you specified (ab)

(b). If you paste the tree string as input to the following HyPhy batch file, it will print out a tree string with the internal node names shown.

Code:

fscanf (stdin, "String", treeString);
Topology T = treeString;
fprintf (stdout, "\n", Format (T,1,1), "\n");

 

Sergei