
 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 = 113
Reading sequences, sequential format..
Reading seq # 1: 1SRN_A     
Reading seq # 2: RNAS1_1     
Reading seq # 3: RNAS1_2     
Reading seq # 4: RNAS1_M     
Reading seq # 5: RNS1B_R     
Sequences read..
Counting site patterns..  0:00

          75 patterns at      113 /      113 sites (100.0%),  0:00
Counting frequencies..

       80 bytes for distance
    24000 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
(((2, 3), (4, 5)), 1);   MP score: 97
This is a rooted tree, without clock.  Check.

    48000 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.055850    0.039823    0.128319    0.092920    0.057522    0.098820    0.148968    0.103442

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 =  -827.743786

Round 1b: Blengths (8, e=1e-08)
	lnL0 =       -827.743786
	Cycle  1:    -821.638194
	Cycle  2:    -821.586647
	Cycle  3:    -821.586132
	Cycle  4:    -821.586129
	Cycle  5:    -821.586129
	Cycle  6:    -821.586129

 0:00

lnL  =  -821.586129
Out..
lnL  =  -821.586129
3 lfun, 0 eigenQcodon, 144 P(t)

Reconstructed ancestral states go into file rst.

lnL =  -821.586129 from ProbSitePattern.
Marginal reconstruction.
	Node   6: lnL =  -821.586129
	Node   7: lnL =  -821.586129
	Node   8: lnL =  -821.586129
	Node   9: lnL =  -821.586129

lnL =  -821.586129 from ProbSitePattern.
Joint reconstruction.

   192000 bytes for conP, adjusted
end of tree file.

Time used:  0:01
