
 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 = 319
Reading sequences, sequential format..
Reading seq # 1: 1SZ2_A     
Reading seq # 2: GLK_ECO     
Reading seq # 3: I0ABJ0     
Reading seq # 4: C9XXD4     
Reading seq # 5: GLK_YER     
Sequences read..
Counting site patterns..  0:00

          98 patterns at      319 /      319 sites (100.0%),  0:00
Counting frequencies..

       80 bytes for distance
    31360 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
((2, (3, (4, 5))), 1);   MP score: 111
This is a rooted tree, without clock.  Check.

    62720 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.000000    0.002303    0.034567    0.039354    0.033319    0.067590    0.143976    0.027492

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 = -1525.672814

Round 1b: Blengths (8, e=1e-08)
	lnL0 =      -1525.672814
	Cycle  1:   -1513.380708
	Cycle  2:   -1513.369359
	Cycle  3:   -1513.368761
	Cycle  4:   -1513.368752
	Cycle  5:   -1513.368752
	Cycle  6:   -1513.368752

 0:00

lnL  = -1513.368752
Out..
lnL  = -1513.368752
3 lfun, 0 eigenQcodon, 144 P(t)

Reconstructed ancestral states go into file rst.

lnL = -1513.368752 from ProbSitePattern.
Marginal reconstruction.
	Node   6: lnL = -1513.368752
	Node   7: lnL = -1513.368752
	Node   8: lnL = -1513.368752
	Node   9: lnL = -1513.368752

lnL = -1513.368752 from ProbSitePattern.
Joint reconstruction.

   250880 bytes for conP, adjusted
end of tree file.

Time used:  0:00
