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CJFIELDS / BioPerl-Run-1.006900 / t / data / codeml.mlc 
AAML (in paml 3.12 February 2002)    stewart.aa   Model: Empirical (wag.dat) 
ns = 6  	ls = 130
# site patterns = 98
    4    1    1    1    1    8    2    1    6    1    1    3    1    1    1
    1    1    4    2    1    1    3    1    4    1    1    1    1    1    1
    3    1    1    1    1    1    1    1    1    1    1    2    2    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1

Langur                KIFERCELAR TLKLGLDGYK VSNWVLAKWG NTETYNPGDE TDYIFQSRYN NGTPGAVDAH ISSALQNNIA DAVARVVSDP QIRVRNHQNK VSQVKGGV
Baboon                .......... ..R......R I........D ..Q......Q .......H.. D......N.. ..N...D..T .......... .........R ....Q...
Human                 .V........ ..R..M...R I...M..... ..R...A..R .......... D......N.. L.....D... .......R.. ......R..R .R..Q...
Rat                   .TY....F.. ..RN.MS..Y ..D....QHN ..QR.D...Q .......... D...R.KN.G .P....DD.T Q.IQ...R.. ....QR.K.R L.GIRN..
Cow                   .V........ .......... ....L.T..S ..K....SS. .......KW. D...N...G. V..EME.D.. K...KI..E- ..T.KS.RDH ..S.E.TL
Horse                 .V.SK....H K.AQEM..FG Y....M.EYN ..RFGKNANG S..L..NKWK DN-RSSSN.N .M.K.DE..D .DIS...R.. KMSKVK.KD. L.ELASNL




Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
Langur                         0.1000 0.0462 0.0846 0.0538 0.0615 0.0385 0.0385 0.0846 0.0154 0.0462 0.0615 0.0692 0.0000 0.0154 0.0231 0.0615 0.0385 0.0385 0.0462 0.0769
Baboon                         0.0923 0.0615 0.0846 0.0692 0.0615 0.0615 0.0231 0.0769 0.0231 0.0538 0.0615 0.0385 0.0000 0.0154 0.0231 0.0538 0.0462 0.0385 0.0462 0.0692
Human                          0.1077 0.1077 0.0769 0.0615 0.0615 0.0462 0.0231 0.0846 0.0077 0.0385 0.0615 0.0385 0.0154 0.0154 0.0154 0.0462 0.0385 0.0385 0.0462 0.0692
Rat                            0.0846 0.0923 0.0692 0.0692 0.0615 0.0692 0.0231 0.0769 0.0154 0.0538 0.0462 0.0462 0.0077 0.0154 0.0308 0.0538 0.0462 0.0308 0.0615 0.0462
Cow                            0.0775 0.0233 0.0620 0.0543 0.0620 0.0155 0.0620 0.0620 0.0233 0.0388 0.0698 0.0930 0.0078 0.0155 0.0155 0.1008 0.0620 0.0465 0.0388 0.0698
Horse                          0.0853 0.0310 0.1008 0.0775 0.0620 0.0155 0.0465 0.0543 0.0155 0.0233 0.0775 0.1163 0.0310 0.0388 0.0078 0.1008 0.0078 0.0388 0.0310 0.0388

Average                        0.0913 0.0604 0.0797 0.0643 0.0617 0.0411 0.0360 0.0733 0.0167 0.0424 0.0630 0.0668 0.0103 0.0193 0.0193 0.0694 0.0398 0.0386 0.0450 0.0617
(Ambiguity characters are used to calculate freqs.)


# constant sites:     46 (35.38%)
AA distances (raw proportions of different sites)

Langur         
Baboon           0.1077
Human            0.1385  0.1077
Rat              0.2923  0.2538  0.2846
Cow              0.2462  0.3000  0.3154  0.4231
Horse            0.5000  0.5000  0.4923  0.4923  0.5462

TREE #  1:  (((1, 2), 3), 4, (5, 6));   MP score: -1
lnL(ntime:  9  np:  9):  -1042.768973     +0.000000
   7..8     8..9     9..1     9..2     8..3     7..4     7..10   10..5    10..6  
  0.00950  0.02220  0.08009  0.03337  0.06233  0.27133  0.09393  0.24105  0.58792

tree length =   1.40172

(((1:0.080088, 2:0.033370):0.022202, 3:0.062325):0.009497, 4:0.271333, (5:0.241055, 6:0.587920):0.093926);

(((Langur:0.080088, Baboon:0.033370):0.022202, Human:0.062325):0.009497, Rat:0.271333, (Cow:0.241055, Horse:0.587920):0.093926);