
 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 = 38  	ls = 1
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

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

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

TREE #  1

Branch lengths in tree are fixed.
((((((((((((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: 14
This is a rooted tree, without clock.  Check.

     5920 bytes for conP, adjusted


Reading matrix from MyModel_214.dat


ntime & nrate & np:     0     0     0

np =     0
lnL0 =   -66.967152
Out..
lnL  =   -66.967152
1 lfun, 0 eigenQcodon, 74 P(t)

Reconstructed ancestral states go into file rst.

lnL =   -66.967152 from ProbSitePattern.
Marginal reconstruction.
	Node  39: lnL =   -66.967152
	Node  40: lnL =   -66.967152
	Node  41: lnL =   -66.967152
	Node  42: lnL =   -66.967152
	Node  43: lnL =   -66.967152
	Node  44: lnL =   -66.967152
	Node  45: lnL =   -66.967152
	Node  46: lnL =   -66.967152
	Node  47: lnL =   -66.967152
	Node  48: lnL =   -66.967152
	Node  49: lnL =   -66.967152
	Node  50: lnL =   -66.967152
	Node  51: lnL =   -66.967152
	Node  52: lnL =   -66.967152
	Node  53: lnL =   -66.967152
	Node  54: lnL =   -66.967152
	Node  55: lnL =   -66.967152
	Node  56: lnL =   -66.967152
	Node  57: lnL =   -66.967152
	Node  58: lnL =   -66.967152
	Node  59: lnL =   -66.967152
	Node  60: lnL =   -66.967152
	Node  61: lnL =   -66.967152
	Node  62: lnL =   -66.967152
	Node  63: lnL =   -66.967152
	Node  64: lnL =   -66.967152
	Node  65: lnL =   -66.967152
	Node  66: lnL =   -66.967152
	Node  67: lnL =   -66.967152
	Node  68: lnL =   -66.967152
	Node  69: lnL =   -66.967152
	Node  70: lnL =   -66.967152
	Node  71: lnL =   -66.967152
	Node  72: lnL =   -66.967152
	Node  73: lnL =   -66.967152
	Node  74: lnL =   -66.967152
	Node  75: lnL =   -66.967152

lnL =   -66.967152 from ProbSitePattern.
Joint reconstruction.

    23680 bytes for conP, adjusted
end of tree file.

Time used:  0:00
