
 15         verbose | verbose                2.00
  7         runmode | runmode                0.00
  4         seqtype | seqtype                2.00
 19      aaRatefile | aaRatefile             1.00
 16           model | model                  2.00
 28       fix_alpha | fix_alpha              1.00
 29           alpha | alpha                  0.00
 30          Malpha | Malpha                 0.00
 32         fix_rho | fix_rho                1.00
 33             rho | rho                    0.00
  9           clock | clock                  0.00
 11           getSE | getSE                  0.00
 36      Small_Diff | Small_Diff             0.00
  6       cleandata | cleandata              0.00
  8          method | method                 1.00
 12    RateAncestor | RateAncestor           1.00
 34           ndata | ndata                  1.00
 37     fix_blength | fix_blength            0.00
AAML in paml version 4.8, March 2014

seq file is not paml/phylip format.  Trying nexus format.
ns = 5  	ls = 419
Reading sequences, sequential format..
Reading seq # 1: 1EY2_A     
Reading seq # 2: HGD_HUM     
Reading seq # 3: B8YB76_B     
Reading seq # 4: HGD_MOU     
Reading seq # 5: Q6AYR0     
Sequences read..
Counting site patterns..  0:00

          67 patterns at      419 /      419 sites (100.0%),  0:00
Counting frequencies..

       80 bytes for distance
    21440 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
((2, (3, (4, 5))), 1);   MP score: 58
This is a rooted tree, without clock.  Check.

    42880 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.000000    0.015537    0.067845    0.028175    0.079794    0.074431    0.042292    0.047593

ntime & nrate & np:     8     0     8

Bounds (np=8):
   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004
  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000

np =     8
lnL0 = -1642.746761

Round 1b: Blengths (8, e=1e-08)
	lnL0 =      -1642.746761
	Cycle  1:   -1588.294423
	Cycle  2:   -1588.202949
	Cycle  3:   -1588.202824
	Cycle  4:   -1588.202824
	Cycle  5:   -1588.202824

 0:00

lnL  = -1588.202824
Out..
lnL  = -1588.202824
3 lfun, 0 eigenQcodon, 124 P(t)

Reconstructed ancestral states go into file rst.

lnL = -1588.202824 from ProbSitePattern.
Marginal reconstruction.
	Node   6: lnL = -1588.202824
	Node   7: lnL = -1588.202824
	Node   8: lnL = -1588.202824
	Node   9: lnL = -1588.202824

lnL = -1588.202824 from ProbSitePattern.
Joint reconstruction.

   171520 bytes for conP, adjusted
end of tree file.

Time used:  0:00
