
 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 = 28  	ls = 1
Reading sequences, sequential format..
Reading seq # 1: TRXB_STAAW_4gcm     
Reading seq # 2: TRXB_BACSU_7_288     
Reading seq # 3: TRXB_LISMO_9_290     
Reading seq # 4: Q9RSY7_DEIRA     
Reading seq # 5: C4LW95_ENTHI_4a5l     
Reading seq # 6: TRXB1_YEAST_3d8x_3itj     
Reading seq # 7: TRXB_CHLTR_5_294     
Reading seq # 8: TRXB_CHLPN_5_294     
Reading seq # 9: TRXB_ECOLI_7_297     
Reading seq #10: TRXB_HAEIN_8_297     
Reading seq #11: Q9I0M2_PSEAE_8_316     
Reading seq #12: Q9JU23_NEIMA_6_316     
Reading seq #13: TRXB_BUCAP_8_299     
Reading seq #14: TRXB_BUCAI_8_299     
Reading seq #15: TRXB_COXBU_8_299     
Reading seq #16: Q8YID2_BRUME     
Reading seq #17: Q9X5F7_ZYMMO_9_294     
Reading seq #18: TRXB_RICPR_6_292     
Reading seq #19: TRXB_MYCTU_16_299     
Reading seq #20: TRXB_MYCLE_13_296     
Reading seq #21: Q9RIS2_STRCO_9_294     
Reading seq #22: TRXB_STRCO_5_289     
Reading seq #23: TRXB_TREPA_6_286     
Reading seq #24: TRXB_MYCPN_17_299     
Reading seq #25: TRXB_MYCGE_17_299     
Reading seq #26: Q0PBZ1_CAMJE     
Reading seq #27: TRXB_HELPY_3_292     
Reading seq #28: Q8X236_SULSF     
Sequences read..
Counting site patterns..  0:00

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

     3024 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), 3), 23), 4), ((26, 27), (28, (24, 25)))), ((19, 20), (21, 22))), (((16, 17), 18), ((13, 14), ((9, 10), (15, (11, 12)))))), (7, 8)), (5, 6));   MP score: 11
This is a rooted tree, without clock.  Check.

     4320 bytes for conP, adjusted


Reading matrix from MyModel_290.dat


ntime & nrate & np:     0     0     0

np =     0
lnL0 =   -58.445780
Out..
lnL  =   -58.445780
1 lfun, 0 eigenQcodon, 54 P(t)

Reconstructed ancestral states go into file rst.

lnL =   -58.445780 from ProbSitePattern.
Marginal reconstruction.
	Node  29: lnL =   -58.445780
	Node  30: lnL =   -58.445780
	Node  31: lnL =   -58.445780
	Node  32: lnL =   -58.445780
	Node  33: lnL =   -58.445780
	Node  34: lnL =   -58.445780
	Node  35: lnL =   -58.445780
	Node  36: lnL =   -58.445780
	Node  37: lnL =   -58.445780
	Node  38: lnL =   -58.445780
	Node  39: lnL =   -58.445780
	Node  40: lnL =   -58.445780
	Node  41: lnL =   -58.445780
	Node  42: lnL =   -58.445780
	Node  43: lnL =   -58.445780
	Node  44: lnL =   -58.445780
	Node  45: lnL =   -58.445780
	Node  46: lnL =   -58.445780
	Node  47: lnL =   -58.445780
	Node  48: lnL =   -58.445780
	Node  49: lnL =   -58.445780
	Node  50: lnL =   -58.445780
	Node  51: lnL =   -58.445780
	Node  52: lnL =   -58.445780
	Node  53: lnL =   -58.445780
	Node  54: lnL =   -58.445780
	Node  55: lnL =   -58.445780

lnL =   -58.445780 from ProbSitePattern.
Joint reconstruction.

    17280 bytes for conP, adjusted
end of tree file.

Time used:  0:00
