
 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 = 43  	ls = 53
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

          48 patterns at       53 /       53 sites (100.0%),  0:00
Counting frequencies..

     7224 bytes for distance
    15360 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1

This is a rooted tree, without clock.  Check.

   1   15.225093
   2   12.357300
   3   11.613826
   4   11.543480
   5   11.526883
   6   11.523933
   7   11.523408
   8   11.523283
   9   11.523267
  10   11.523264
   322560 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.066357    0.010686    0.080010    0.082484    0.064565    0.123709    0.093651    0.051089    0.105303    0.092081    0.069029    0.017695    0.031018    0.012586    0.022157    0.171370    0.095634    0.089625    0.037766    0.093654    0.048117    0.105719    0.046163    0.072116    0.014875    0.095436    0.069574    0.030632    0.147602    0.006805    0.121774    0.014644    0.167619    0.163566    0.063524    0.091224    0.103800    0.119572    0.053606    0.078739    0.071159    0.063563    0.015231    0.028528    0.145556    0.098343    0.164718    0.000000    0.097709    0.106396    0.084416    0.146127    0.108579    0.054087    0.112666    0.080112    0.033214    0.037973    0.030476    0.043945    0.047985    0.043126    0.090111    0.052954    0.105089    0.075949    0.017397    0.041735    0.062944    0.090359    0.050456    0.126029    0.034294    0.056502    0.095467    0.030070    0.075293    0.089042    0.005016    0.168640    0.020841    0.066883    0.118931    0.099914

ntime & nrate & np:    84     0    84

Bounds (np=84):
   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   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  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000

np =    84
lnL0 = -2835.546383

Round 1b: Blengths (84, e=1e-08)
	lnL0 =      -2835.546383
	Cycle  1:   -2642.800708
	Cycle  2:   -2631.041498
	Cycle  3:   -2630.486493
	Cycle  4:   -2630.449034
	Cycle  5:   -2630.442791
	Cycle  6:   -2630.441910
	Cycle  7:   -2630.441768
	Cycle  8:   -2630.441744
	Cycle  9:   -2630.441740
	Cycle 10:   -2630.441739
	Cycle 11:   -2630.441739
	Cycle 12:   -2630.441739
	Cycle 13:   -2630.441739

 0:00

lnL  = -2630.441739
Out..
lnL  = -2630.441739
3 lfun, 0 eigenQcodon, 3476 P(t)

Reconstructed ancestral states go into file rst.

lnL = -2630.441739 from ProbSitePattern.
Marginal reconstruction.
	Node  44: lnL = -2630.441739
	Node  45: lnL = -2630.441739
	Node  46: lnL = -2630.441739
	Node  47: lnL = -2630.441739
	Node  48: lnL = -2630.441739
	Node  49: lnL = -2630.441739
	Node  50: lnL = -2630.441739
	Node  51: lnL = -2630.441739
	Node  52: lnL = -2630.441739
	Node  53: lnL = -2630.441739
	Node  54: lnL = -2630.441739
	Node  55: lnL = -2630.441739
	Node  56: lnL = -2630.441739
	Node  57: lnL = -2630.441739
	Node  58: lnL = -2630.441739
	Node  59: lnL = -2630.441739
	Node  60: lnL = -2630.441739
	Node  61: lnL = -2630.441739
	Node  62: lnL = -2630.441739
	Node  63: lnL = -2630.441739
	Node  64: lnL = -2630.441739
	Node  65: lnL = -2630.441739
	Node  66: lnL = -2630.441739
	Node  67: lnL = -2630.441739
	Node  68: lnL = -2630.441739
	Node  69: lnL = -2630.441739
	Node  70: lnL = -2630.441739
	Node  71: lnL = -2630.441739
	Node  72: lnL = -2630.441739
	Node  73: lnL = -2630.441739
	Node  74: lnL = -2630.441739
	Node  75: lnL = -2630.441739
	Node  76: lnL = -2630.441739
	Node  77: lnL = -2630.441739
	Node  78: lnL = -2630.441739
	Node  79: lnL = -2630.441739
	Node  80: lnL = -2630.441739
	Node  81: lnL = -2630.441739
	Node  82: lnL = -2630.441739
	Node  83: lnL = -2630.441739
	Node  84: lnL = -2630.441739
	Node  85: lnL = -2630.441739

lnL = -2630.441739 from ProbSitePattern.
Joint reconstruction.

  1290240 bytes for conP, adjusted
end of tree file.

Time used:  0:02
