To obtain help on running these programs, execute them on the command
line with the "--help" option.

Source Code

The source code for the implementation of the polytope-propagation
algorithm is available as part of Colin
Dewey's source code package. Source code for the beneath-beyond
implementation will be made available soon.

Scoring Matrices

The parametric alignment programs can take as input a symbolic scoring
matrix. The default scoring scheme is the Jukes-Cantor scoring matrix
with affine gap scores (a 3d model). Here are matrices for the phylogenetic models
JC69, K80, K81, SYM.