This is the FastCodeML evaluation package including sources and a precompiled executable. This package is currently for evaluation purposes only. 

Usage, e.g.:
./fast -m 22 -bf -hy 0  ENSGT00390000016702.Primates.01.002.nwk  ENSGT00390000016702.Primates.01.phy
Above execution estimates the log likelihood for hypothesis 0 and the foreground specified in the Newick file. The output could be like the following:
===
Doing branch 0
Check ming2 convergence

LnL0: -2393.120011398410952 Function calls: 1235   

  0.2724265  0.1727072  0.2111106  0.0443093  0.0160066  0.0102474  0.0050577  0.0084463
  0.0254361  0.1328335  0.0754612

p0:  0.4817192  p1:  0.5182808  p2a:  0.0000000  p2b:  0.0000000
w0:  0.0000010  k:   5.1561778
===

Please always use optimisation method "-m22" on the command line, as the other optimisers are still under investigation and not discussed in the paper.

Read INSTALL for installation instructions!
