
 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..

		Are these a.a. sequences?

     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: 6
This is a rooted tree, without clock.  Check.

     5920 bytes for conP, adjusted


Reading matrix from MyModel_96.dat


ntime & nrate & np:     0     0     0

np =     0
lnL0 =   -31.208734
Out..
lnL  =   -31.208734
1 lfun, 0 eigenQcodon, 74 P(t)

Reconstructed ancestral states go into file rst.

lnL =   -31.208734 from ProbSitePattern.
Marginal reconstruction.
	Node  39: lnL =   -31.208734
	Node  40: lnL =   -31.208734
	Node  41: lnL =   -31.208734
	Node  42: lnL =   -31.208734
	Node  43: lnL =   -31.208734
	Node  44: lnL =   -31.208734
	Node  45: lnL =   -31.208734
	Node  46: lnL =   -31.208734
	Node  47: lnL =   -31.208734
	Node  48: lnL =   -31.208734
	Node  49: lnL =   -31.208734
	Node  50: lnL =   -31.208734
	Node  51: lnL =   -31.208734
	Node  52: lnL =   -31.208734
	Node  53: lnL =   -31.208734
	Node  54: lnL =   -31.208734
	Node  55: lnL =   -31.208734
	Node  56: lnL =   -31.208734
	Node  57: lnL =   -31.208734
	Node  58: lnL =   -31.208734
	Node  59: lnL =   -31.208734
	Node  60: lnL =   -31.208734
	Node  61: lnL =   -31.208734
	Node  62: lnL =   -31.208734
	Node  63: lnL =   -31.208734
	Node  64: lnL =   -31.208734
	Node  65: lnL =   -31.208734
	Node  66: lnL =   -31.208734
	Node  67: lnL =   -31.208734
	Node  68: lnL =   -31.208734
	Node  69: lnL =   -31.208734
	Node  70: lnL =   -31.208734
	Node  71: lnL =   -31.208734
	Node  72: lnL =   -31.208734
	Node  73: lnL =   -31.208734
	Node  74: lnL =   -31.208734
	Node  75: lnL =   -31.208734

lnL =   -31.208734 from ProbSitePattern.
Joint reconstruction.

    23680 bytes for conP, adjusted
end of tree file.

Time used:  0:00
