
 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 = 38  	ls = 251
Reading sequences, sequential format..
Reading seq # 1: DNAK_ECOLI_3_603     
Reading seq # 2: DNAK_SALTY_3_603     
Reading seq # 3: DNAK_HAEIN_3_602     
Reading seq # 4: DNAK_BUCAI_4_604     
Reading seq # 5: DNAK_BUCBP_4_604     
Reading seq # 6: DNAK_VIBCH_4_603     
Reading seq # 7: DNAK_COXBU_4_609     
Reading seq # 8: DNAK_HELPY_3_599     
Reading seq # 9: DNAK_CAMJE_4_600     
Reading seq #10: DNAK_RHIME_4_601     
Reading seq #11: DNAK_CAUCR_4_598     
Reading seq #12: DNAK_RICPR_4_598     
Reading seq #13: DNAK_BORBU_4_599     
Reading seq #14: DNAK_TREPA_4_598     
Reading seq #15: DNAK_LACLC_4_574     
Reading seq #16: DNAK_STRMU_4_575     
Reading seq #17: DNAK_STRPN_4_574     
Reading seq #18: DNAK_STRPY_4_574     
Reading seq #19: DNAK_BACSU_3_573     
Reading seq #20: DNAK_BACST_3_572     
Reading seq #21: DNAK_LISMO_4_574     
Reading seq #22: DNAK_MYCTU_3_582     
Reading seq #23: DNAK_MYCLE_3_583     
Reading seq #24: DNAK_CLOPE_4_575     
Reading seq #25: DNAK_CHLTR_9_602     
Reading seq #26: DNAK_CHLMU_9_602     
Reading seq #27: DNAK_CHLPN_10_603     
Reading seq #28: DNAK_AQUAE_8_606     
Reading seq #29: DNAK_PORPU_4_597     
Reading seq #30: DNAK_GUITH_4_599     
Reading seq #31: DNAK_PAVLU_4_601     
Reading seq #32: DNAK_CYACA_4_599     
Reading seq #33: DNAK_THEMA_8_586     
Reading seq #34: DNAK_THEAC_4_581     
Reading seq #35: DNAK_THETH_4_597     
Reading seq #36: DNAK_MYCGE_8_593     
Reading seq #37: DNAK_MYCPN_8_586     
Reading seq #38: HSP71_HUMAN     
Sequences read..
Counting site patterns..  0:00

         214 patterns at      251 /      251 sites (100.0%),  0:00
Counting frequencies..

     5624 bytes for distance
    68480 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
((((((((((((1, 2), (4, 5)), 6), 3), 7), (8, 9)), (12, (10, 11))), (24, (21, ((19, 20), (15, (18, (16, 17))))))), (13, 14)), (((25, 26), 27), (28, (((36, 37), 35), ((33, 34), (32, (30, (29, 31)))))))), (22, 23)), 38);   MP score: -1
This is a rooted tree, without clock.  Check.

   1    8.432897
   2    5.464772
   3    4.818691
   4    4.680845
   5    4.648927
   6    4.648748
   7    4.648734
   8    4.648733
  1266880 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.129944    0.012153    0.030957    0.000397    0.039099    0.035004    0.022336    0.044720    0.026823    0.022197    0.076085    0.020901    0.018758    0.028044    0.072838    0.092514    0.120658    0.092921    0.119013    0.039514    0.128819    0.102802    0.024296    0.099968    0.014700    0.102900    0.112227    0.013763    0.164671    0.053508    0.085960    0.007858    0.040964    0.066683    0.074720    0.040951    0.061156    0.064049    0.049867    0.029848    0.065924    0.028958    0.041651    0.095739    0.100924    0.009610    0.119840    0.048255    0.036405    0.040396    0.059215    0.049390    0.174376    0.018155    0.035903    0.167545    0.025711    0.028006    0.162189    0.010404    0.029406    0.164740    0.152489    0.061994    0.135336    0.032080    0.094867    0.000000    0.109540    0.131858    0.137463    0.045449    0.033929    0.175716

ntime & nrate & np:    74     0    74

Bounds (np=74):
   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

np =    74
lnL0 = -9798.254134

Round 1b: Blengths (74, e=1e-08)
	lnL0 =      -9798.254134
	Cycle  1:   -9447.584963
	Cycle  2:   -9432.380648
	Cycle  3:   -9431.865923
	Cycle  4:   -9431.851556
	Cycle  5:   -9431.851041
	Cycle  6:   -9431.851015
	Cycle  7:   -9431.851012
	Cycle  8:   -9431.851012
	Cycle  9:   -9431.851012
	Cycle 10:   -9431.851012

 0:01

lnL  = -9431.851012
Out..
lnL  = -9431.851012
3 lfun, 0 eigenQcodon, 2402 P(t)

Reconstructed ancestral states go into file rst.

lnL = -9431.851012 from ProbSitePattern.
Marginal reconstruction.
	Node  39: lnL = -9431.851012
	Node  40: lnL = -9431.851012
	Node  41: lnL = -9431.851012
	Node  42: lnL = -9431.851012
	Node  43: lnL = -9431.851012
	Node  44: lnL = -9431.851012
	Node  45: lnL = -9431.851012
	Node  46: lnL = -9431.851012
	Node  47: lnL = -9431.851012
	Node  48: lnL = -9431.851012
	Node  49: lnL = -9431.851012
	Node  50: lnL = -9431.851012
	Node  51: lnL = -9431.851012
	Node  52: lnL = -9431.851012
	Node  53: lnL = -9431.851012
	Node  54: lnL = -9431.851012
	Node  55: lnL = -9431.851012
	Node  56: lnL = -9431.851012
	Node  57: lnL = -9431.851012
	Node  58: lnL = -9431.851012
	Node  59: lnL = -9431.851012
	Node  60: lnL = -9431.851012
	Node  61: lnL = -9431.851012
	Node  62: lnL = -9431.851012
	Node  63: lnL = -9431.851012
	Node  64: lnL = -9431.851012
	Node  65: lnL = -9431.851012
	Node  66: lnL = -9431.851012
	Node  67: lnL = -9431.851012
	Node  68: lnL = -9431.851012
	Node  69: lnL = -9431.851012
	Node  70: lnL = -9431.851012
	Node  71: lnL = -9431.851012
	Node  72: lnL = -9431.851012
	Node  73: lnL = -9431.851012
	Node  74: lnL = -9431.851012
	Node  75: lnL = -9431.851012

lnL = -9431.851012 from ProbSitePattern.
Joint reconstruction.

  5067520 bytes for conP, adjusted
end of tree file.

Time used:  0:08
