maxAlike v1.0

Compiling:
- make sure that the library bio++ 1.9 is installed (incl. header files), download from http://kimura.univ-montp2.fr/BioPP/
- compile by typing 'make'

Running:
- run the binary 'maxAlike'

Documentation
-------------
Find help and example on the maxAlike web server at http://rth.dk/resources/maxAlike/

Required Parameters
-------------------
maxAlike expects at least two input files: a multiple sequence alignment (Stockholm format)  and an phylogenetic tree (Newick format)
Example: maxAlike -a myalignment.stk -t mytree.ph

The sequence names in the alignment must match the names of the leaf nodes in the tree. The tree must not contain
multifurcations and have branch lengths on each edge.

If there is only one name in the tree file, which is not in the alignment file, then maxAlike will use this name as
the target for the sequence reconstruction.
If more than one names in the tree have no corresponding entry in the alignment, then the target has to explicitly named 
using the -n option.
Example: maxAlike -a myalignment.stk -t mytree.ph -n targetname

Additional Parameters
---------------------
By default, all positions in the alignment will be calculated. A certain region can be selected with the -x and -y options.
Example: maxAlike -a myalignment.stk -t mytree.ph -n targetname -x 10 -y 25
Only the columns from 10 to 25 will we calculated.
The index of the first column is zero.

The transition bias parameter kappa of the HKY85 substitution model can be set with the -k option.
Example:  maxAlike -a myalignment.stk -t mytree.ph -n targetname -k 2.45
The default is 1.0, i.e. no difference between transition and transversion.

The maximum column-specific mutation rate mu, can be set with the -m option.
Example: maxAlike -a myalignment.stk -t mytree.ph -n targetname -m 2.0
The default is 5.0.

