
 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 = 25  	ls = 1
Reading sequences, sequential format..
Reading seq # 1: TRPA_VIBCH     
Reading seq # 2: TRPA_VIBPA_8_267     
Reading seq # 3: H1AFK5_SHEFR     
Reading seq # 4: TRPA_SALTY_8_267     
Reading seq # 5: TRPA_ECOLI_8_267     
Reading seq # 6: TRPA_KLEAE_8_267     
Reading seq # 7: TRPA_HAEIN_8_268     
Reading seq # 8: TRPA_BUCSC_14_267     
Reading seq # 9: TRPA_BUCBP_9_268     
Reading seq #10: TRPA_BUCAP_8_267     
Reading seq #11: TRPA_BUCDN_8_267     
Reading seq #12: TRPA_HELPY_7_261     
Reading seq #13: TRPA_HELPJ_7_261     
Reading seq #14: TRPA_METTM_7_262     
Reading seq #15: TRPA_METTH_13_268     
Reading seq #16: TRP_YEAST_9_272     
Reading seq #17: TRPA_PSEPU_8_265     
Reading seq #18: TRPA_PSESY_8_265     
Reading seq #19: TRPA_PSEAE_8_265     
Reading seq #20: TRPA_RHOSH_8_261     
Reading seq #21: TRPA_CAUCR_10_268     
Reading seq #22: TRPA_STRCO_10_268     
Reading seq #23: TRPA_MYCTU_16_265     
Reading seq #24: TRPA_MYCIT_15_265     
Reading seq #25: TRPA_THETH_7_267     
Sequences read..
Counting site patterns..  0:00

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

     2400 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), 7), (4, (5, 6))), ((8, 9), (10, 11))), (12, 13)), (14, 15)), (21, (20, (17, (18, 19))))), (25, (22, (23, 24)))), 16);   MP score: -1
This is a rooted tree, without clock.  Check.

     3840 bytes for conP, adjusted


Reading matrix from MyModel_5.dat


ntime & nrate & np:     0     0     0

np =     0
lnL0 =    -9.739628
Out..
lnL  =    -9.739628
1 lfun, 0 eigenQcodon, 48 P(t)

Reconstructed ancestral states go into file rst.

lnL =    -9.739628 from ProbSitePattern.
Marginal reconstruction.
	Node  26: lnL =    -9.739628
	Node  27: lnL =    -9.739628
	Node  28: lnL =    -9.739628
	Node  29: lnL =    -9.739628
	Node  30: lnL =    -9.739628
	Node  31: lnL =    -9.739628
	Node  32: lnL =    -9.739628
	Node  33: lnL =    -9.739628
	Node  34: lnL =    -9.739628
	Node  35: lnL =    -9.739628
	Node  36: lnL =    -9.739628
	Node  37: lnL =    -9.739628
	Node  38: lnL =    -9.739628
	Node  39: lnL =    -9.739628
	Node  40: lnL =    -9.739628
	Node  41: lnL =    -9.739628
	Node  42: lnL =    -9.739628
	Node  43: lnL =    -9.739628
	Node  44: lnL =    -9.739628
	Node  45: lnL =    -9.739628
	Node  46: lnL =    -9.739628
	Node  47: lnL =    -9.739628
	Node  48: lnL =    -9.739628
	Node  49: lnL =    -9.739628

lnL =    -9.739628 from ProbSitePattern.
Joint reconstruction.

    15360 bytes for conP, adjusted
end of tree file.

Time used:  0:00
