
 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            2.00
AAML in paml version 4.8, March 2014

seq file is not paml/phylip format.  Trying nexus format.
ns = 43  	ls = 1
Reading sequences, sequential format..
Reading seq # 1: RUBRCHL1     
Reading seq # 2: RUBRDES2     
Reading seq # 3: RUBRDES3     
Reading seq # 4: Q46496DE     
Reading seq # 5: RUBRBUT5     
Reading seq # 6: RUBRHEL6     
Reading seq # 7: RUBR2CL5     
Reading seq # 8: RUBRPYR6     
Reading seq # 9: P96745C8     
Reading seq #10: RUBRCLO3     
Reading seq #11: RUBRCLO4     
Reading seq #12: RUBRTHE8     
Reading seq #13: O26259ME     
Reading seq #14: RUBRMEG1     
Reading seq #15: O28920AR     
Reading seq #16: RUBRACI5     
Reading seq #17: O05893M3     
Reading seq #18: RUBR1ME1     
Reading seq #19: RUBR1DE4     
Reading seq #20: RUBRMET2     
Reading seq #21: P94698D1     
Reading seq #22: RUBR2ME7     
Reading seq #23: RUBR2PS2     
Reading seq #24: O05894MY     
Reading seq #25: RUBR2PS8     
Reading seq #26: RUBR1PS9     
Reading seq #27: RUBRSYN4     
Reading seq #28: RUBRTRE1     
Reading seq #29: NORVECO1     
Reading seq #30: RUBLRHIg     
Reading seq #31: RUBLBRAJ     
Reading seq #32: HUPJRHOC     
Reading seq #33: RUBRAZO6     
Reading seq #34: RUBRCUP7     
Reading seq #35: P955009P     
Reading seq #36: RUBRPEP7     
Reading seq #37: O50375ME     
Reading seq #38: RUBHMET1     
Reading seq #39: O26576M1     
Reading seq #40: O29905A1     
Reading seq #41: O27972A1     
Reading seq #42: O26912M1     
Reading seq #43: O29906AR     
Sequences read..
Counting site patterns..  0:00

           1 patterns at        1 /        1 sites (100.0%),  0:00
Counting frequencies..

     7224 bytes for distance
      320 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1

Branch lengths in tree are fixed.

This is a rooted tree, without clock.  Check.

     6720 bytes for conP, adjusted


Reading matrix from MyModel_5.dat


ntime & nrate & np:     0     0     0

np =     0
lnL0 =   -83.261002
Out..
lnL  =   -83.261002
1 lfun, 0 eigenQcodon, 84 P(t)

Reconstructed ancestral states go into file rst.

lnL =   -83.261002 from ProbSitePattern.
Marginal reconstruction.
	Node  44: lnL =   -83.261002
	Node  45: lnL =   -83.261002
	Node  46: lnL =   -83.261002
	Node  47: lnL =   -83.261002
	Node  48: lnL =   -83.261002
	Node  49: lnL =   -83.261002
	Node  50: lnL =   -83.261002
	Node  51: lnL =   -83.261002
	Node  52: lnL =   -83.261002
	Node  53: lnL =   -83.261002
	Node  54: lnL =   -83.261002
	Node  55: lnL =   -83.261002
	Node  56: lnL =   -83.261002
	Node  57: lnL =   -83.261002
	Node  58: lnL =   -83.261002
	Node  59: lnL =   -83.261002
	Node  60: lnL =   -83.261002
	Node  61: lnL =   -83.261002
	Node  62: lnL =   -83.261002
	Node  63: lnL =   -83.261002
	Node  64: lnL =   -83.261002
	Node  65: lnL =   -83.261002
	Node  66: lnL =   -83.261002
	Node  67: lnL =   -83.261002
	Node  68: lnL =   -83.261002
	Node  69: lnL =   -83.261002
	Node  70: lnL =   -83.261002
	Node  71: lnL =   -83.261002
	Node  72: lnL =   -83.261002
	Node  73: lnL =   -83.261002
	Node  74: lnL =   -83.261002
	Node  75: lnL =   -83.261002
	Node  76: lnL =   -83.261002
	Node  77: lnL =   -83.261002
	Node  78: lnL =   -83.261002
	Node  79: lnL =   -83.261002
	Node  80: lnL =   -83.261002
	Node  81: lnL =   -83.261002
	Node  82: lnL =   -83.261002
	Node  83: lnL =   -83.261002
	Node  84: lnL =   -83.261002
	Node  85: lnL =   -83.261002

lnL =   -83.261002 from ProbSitePattern.
Joint reconstruction.

    26880 bytes for conP, adjusted
end of tree file.

Time used:  0:00
