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update PAML test resource test.out

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commit 724d8d4f17c2658e122d6c3c0234e604e2534541 1 parent d343179
@brandoninvergo authored
Showing with 16 additions and 31 deletions.
  1. +16 −31 Tests/PAML/Results/test.out
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47 Tests/PAML/Results/test.out
@@ -23,44 +23,29 @@ Macaca_mul ACCGTACT
82 35 1 59 1 1 1 42
+AAML (in paml version 4.5, December 2011) PAML/Alignments/alignment.phylip
+Model: Empirical_F for branches (jones.dat) ns = 5 ls = 222
+
-BASEML (in paml version 4.5, December 2011) PAML/Alignments/alignment.phylip JC69
Frequencies..
- T C A G
-Homo_sapie 0.2027 0.1622 0.3694 0.2658
-Pan_troglo 0.1982 0.1667 0.3694 0.2658
-Gorilla_go 0.2072 0.1577 0.3694 0.2658
-Pongo_pygm 0.2027 0.1622 0.3694 0.2658
-Macaca_mul 0.1937 0.1667 0.3739 0.2658
+ A R N D C Q E G H I L K M F P S T W Y V
+Homo_sapie 0.3694 0.0000 0.0000 0.0000 0.1622 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2027 0.0000 0.0000 0.0000
+Pan_troglo 0.3694 0.0000 0.0000 0.0000 0.1667 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1982 0.0000 0.0000 0.0000
+Gorilla_go 0.3694 0.0000 0.0000 0.0000 0.1577 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2072 0.0000 0.0000 0.0000
+Pongo_pygm 0.3694 0.0000 0.0000 0.0000 0.1622 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2027 0.0000 0.0000 0.0000
+Macaca_mul 0.3739 0.0000 0.0000 0.0000 0.1667 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1937 0.0000 0.0000 0.0000
Homogeneity statistic: X2 = 0.00092 G = 0.00092
-Average 0.2009 0.1631 0.3703 0.2658
+Average 0.3703 0.0000 0.0000 0.0000 0.1631 0.0000 0.0000 0.2658 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2009 0.0000 0.0000 0.0000
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
+AA distances (raw proportions of different sites)
-Printing out site pattern counts
-
- 5 4 P
-
-Homo_sapie TTTT
-Pan_troglo TTCT
-Gorilla_go TCTT
-Pongo_pygm TTTT
-Macaca_mul TTTC
-
-
-
- 218 1 1 2
-
-
-Distances: JC69 (alpha set at 0.00)
-This matrix is not used in later m.l. analysis.
-
-Homo_sapie
-Pan_troglo 0.0045
-Gorilla_go 0.0045 0.0091
-Pongo_pygm 0.0000 0.0045 0.0045
-Macaca_mul 0.0091 0.0136 0.0136 0.0091
+Homo_sapie
+Pan_troglo 0.0045
+Gorilla_go 0.0045 0.0090
+Pongo_pygm 0.0000 0.0045 0.0045
+Macaca_mul 0.0090 0.0135 0.0135 0.0090
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