
 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 = 25  	ls = 276
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

         269 patterns at      276 /      276 sites (100.0%),  0:00
Counting frequencies..

     2400 bytes for distance
    86080 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
((((((((((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.

   1    1.589702
   2    0.887738
   3    0.787780
   4    0.766454
   5    0.761516
   6    0.761360
   7    0.761345
   8    0.761341
   9    0.761341
  1032960 bytes for conP, adjusted


Reading matrix from GlobalMatrixProt_Evol.dat
    0.100155    0.013933    0.071252    0.046130    0.040781    0.055737    0.000000    0.048814    0.053577    0.108204    0.108112    0.144880    0.182043    0.072794    0.083521    0.039443    0.064586    0.052258    0.053496    0.051129    0.163272    0.145755    0.038654    0.122334    0.122738    0.203856    0.034781    0.030831    0.153446    0.064122    0.062750    0.045907    0.181846    0.012997    0.171573    0.077368    0.086800    0.038659    0.089393    0.093367    0.029588    0.215201    0.033159    0.194901    0.156771    0.058108    0.070743    0.146721

ntime & nrate & np:    48     0    48

Bounds (np=48):
   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

np =    48
lnL0 = -9824.623472

Round 1b: Blengths (48, e=1e-08)
	lnL0 =      -9824.623472
	Cycle  1:   -9380.903450
	Cycle  2:   -9355.012826
	Cycle  3:   -9354.701090
	Cycle  4:   -9354.654579
	Cycle  5:   -9354.645585
	Cycle  6:   -9354.643655
	Cycle  7:   -9354.643231
	Cycle  8:   -9354.643138
	Cycle  9:   -9354.643117
	Cycle 10:   -9354.643112
	Cycle 11:   -9354.643111
	Cycle 12:   -9354.643111
	Cycle 13:   -9354.643111
	Cycle 14:   -9354.643111
	Cycle 15:   -9354.643111

 0:01

lnL  = -9354.643111
Out..
lnL  = -9354.643111
3 lfun, 0 eigenQcodon, 2244 P(t)

Reconstructed ancestral states go into file rst.

lnL = -9354.643111 from ProbSitePattern.
Marginal reconstruction.
	Node  26: lnL = -9354.643111
	Node  27: lnL = -9354.643111
	Node  28: lnL = -9354.643111
	Node  29: lnL = -9354.643111
	Node  30: lnL = -9354.643111
	Node  31: lnL = -9354.643111
	Node  32: lnL = -9354.643111
	Node  33: lnL = -9354.643111
	Node  34: lnL = -9354.643111
	Node  35: lnL = -9354.643111
	Node  36: lnL = -9354.643111
	Node  37: lnL = -9354.643111
	Node  38: lnL = -9354.643111
	Node  39: lnL = -9354.643111
	Node  40: lnL = -9354.643111
	Node  41: lnL = -9354.643111
	Node  42: lnL = -9354.643111
	Node  43: lnL = -9354.643111
	Node  44: lnL = -9354.643111
	Node  45: lnL = -9354.643111
	Node  46: lnL = -9354.643111
	Node  47: lnL = -9354.643111
	Node  48: lnL = -9354.643111
	Node  49: lnL = -9354.643111

lnL = -9354.643111 from ProbSitePattern.
Joint reconstruction.

  4131840 bytes for conP, adjusted
end of tree file.

Time used:  0:06
