fastcodeml/README at master · mrrlab/fastcodeml · GitHub

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

Read INSTALL for installation instructions!

Usage, e.g.:

./fast -m 22 -bl -nt 1 -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 using only one thread. The output could be like the following:

===

Doing foreground branch(es) from tree file
-------------------------------------------
Doing foreground branch(es)  0

LnL0: -2393.300017592994664 Function calls: 365

  0.2544410  0.1691760  0.1998330  0.0446050  0.0153330  0.0101750  0.0050080  0.0084390
  0.0253000  0.1309500  0.0743030

p0:  0.4858354  p1:  0.5141646  p2a:  0.0000000  p2b:  0.0000000
w0:  0.0000010  k:   5.1252258


Final Annotated Newick Tree (*N marks the branch N)

((a001:0.169176*1,a002:0.199833*2)#1:0.254441*0,(((a003:0.005008*6,a004:0.008439*7):0.010175*5,a005:0.025300*8):0.015333*4,a006:0.130950*9):0.044605*3,a007:0.074303*10):0.000000;

((a001:0.169176,a002:0.199833)#1:0.254441,(((a003:0.005008,a004:0.008439):0.010175,a005:0.025300):0.015333,a006:0.130950):0.044605,a007:0.074303):0.000000;

Time used: 0m:22s
Cores used: 1

===