 32                                                                         
  2   4                                                                     
 11   0 864                                                                 
  0 186   0   0                                                             
  0 246   8  49   0                                                         
  0   0   0 569   0 274                                                     
 78  18  47  79   0   0  22                                                 
  8 232 458  11 305 550  22   0                                             
 75   0  19   0  41   0   0   0   0                                         
 21   6   0   0  27  20   0   0  26 232                                     
  0  50 408   0   0 242 215   0   0   6   4                                 
 76   0  21   0   0  22   0   0   0 378 609  59                             
  0   0   6   5   7   0   0   0   0  57 246   0  11                         
 53   9  33   2   0  51   0   0  53   5  43  18   0  17                     
342   3 446  16 347  30  21 112  20   0  74  65  47  90 202                 
681   0 110   0 114   0   4   0   1 360  34  50 691   8  78 614             
  5  16   6   0  65   0   0   0   0   0  12   0  13   0   7  17   0         
  0   0 156   0 530  54   0   1 1525 16  25  67   0 682   8 107   0  14    
398   0   0  10   0  33  20   5   0 2220 100  0 832   6   0   0 237   0   0


0.0692 0.0184 0.0400 0.0186 0.0065 0.0238 0.0236 0.0557 0.0277 0.0905
0.1675 0.0221 0.0561 0.0611 0.0536 0.0725 0.0870 0.0293 0.0340 0.0428

// this is the end of the file.  The rest are notes.

 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val


Symmetrical part of the rate matrix and aa frequencies, estimated from
the 12 mt proteins (atp6 atp8 cox1 cox2 cox3 cytb nd1 nd2 nd3 nd4 nd4l
nd5) on the same strand of the mitochondrial DNA (3331 sites).  The
data are from 20 species of mammals and three close outgroups
(wallaroo, opossum, and platypus).  The model used is
REVaa+dGamma(K=8) with the estimated gamma parameter to be 0.37.  The
first part is S_ij = S_ji, and the second part has the amino acid
frequencies (PI_i).  The substitution rate from amino acid i to j is
Q_ij=S_ij*PI_j.


The data are from

   Cao, Y. et al. 1998 Conflict amongst individual mitochondrial proteins
   in resolving the phylogeny of eutherian orders.  Journal of
   Molecular Evolution 15:1600-1611.

The species are listed below

1 SB17F Homo sapiens (African) # D38112
2 CHIMP Pan troglodytes (chimpanzee) # D38113
3 PyGC Pan paniscus (bonobo) # D38116
4 GORIL Gorilla gorilla (gorilla) # D38114
5 ORANG Pongo pygmaeus (orangutan) # D38115
6 Ponpy Pongo pygmaeus abelii (Sumatran orangutan) # X97707
7 Hylla Hylobates lar (common gibbon) # X99256 (lar gibbon)
8 Phovi Phoca vitulina (harbor seal) # X63726
9 Halgr Halichoerus grypus (grey seal) # X72004
10 Felca Felis catus (cat) # U20753
11 Equca Equus caballus (horse) # X79547
12 Rhiun Rhinoceros unicornis (Indian rhinoceros) # X97336
13 Bosta Bos taurus (cow) # J01394
14 Balph Balaenoptera physalus (fin whale) # X61145
15 Balmu Balaenoptera musculus (blue whale) # X72204
16 Ratno Rattus norvegicus (rat) # X14848
17 Musmu Mus musculus (mouse) # J01420
18 Macro Macropus robustus (wallaroo) # Y10524
19 Didvi Didelphis virginiana (opossum) # Z29573
20 Ornan Ornithorhynchus anatinus (platypus) # X83427


The results are details of the model are published in

   Yang, Z., R. Nielsen, and M. Hasegawa.  1998.  Models of amino acid
   substitution and applications to Mitochondrial protein evolution, 
   Molecular Biology and Evolution 15:1600-1611.

Prepared by Z. Yang, April 1998.
