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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 ===