new standard RAxML version with marginal ancestral state computation

[Alexis]

Dear All,

I just pushed a new version of standard RAxML to the GIT that computes
marginal ancestral states (see Ziheng Yang's book for details).

For marginal ancestral state reconstructions you need to pass a rooted
tree to RAxML.

To invoke, type for instance:

./raxmlHPC-SSE3 -f A -t testTree -s testData -m BINGAMMA -n T1

with the small test alignment:

4 4
t1 0101
t2 0111
t3 0100
t4 0110

and a test tree:

((t1,t2),(t3,t4));

RAxML will then output a rooted binary tree again with inner node
labels and two files
containing the marginal probabilities for each inner root label as
well as a guess for the ancestral sequence.

The code should work for all data types, partitioned datasets etc.

Once again, latest code updates are available at:

https://github.com/stamatak/standard-RAxML

Have fun,

Alexis