************************************************************
     LAMARC:  Maximum Likelihood Parameter Estimation
    using Hastings-Metropolis Markov Chain Monte Carlo
************************************************************
version 2.1.8


        Program started on Tue May 29 11:48:08 2012
                finished on Tue May 29 11:48:20 2012

===========================================================================
Maximum Likelihood Estimates (MLEs) of Parameters
===========================================================================


                 Theta   
Population       Theta1  
Best Val (MLE)  0.020756 
    Percentile           
   99%   0.005  0.013896 
   95%   0.025  0.015231 
   90%   0.050  0.015979 
   75%   0.125  0.017250 
   50%   0.250  0.018600 
           MLE  0.020756 
   50%   0.750  0.023245 
   75%   0.875  0.025235 
   90%   0.950  0.027541 
   95%   0.975  0.029154 
   99%   0.995  0.032670 
Theta1:  Theta for ZMNE



===========================================================================
Profile Likelihoods
===========================================================================

===========================================================================
                           Overall Profile Tables                          
===========================================================================

Overall: Theta for ZMNE (Theta1):
---------------------------------

Percentile profile: Points shown indicate approximate confidence
  intervals.

Log Likelihoods:

Percentile  Theta1   |   Ln(L)   
  0.005    0.013896  | -3.309203 
  0.025    0.015231  | -1.912364 
  0.050    0.015979  | -1.344435 
  0.125    0.017250  | -0.653339 
  0.250    0.018600  | -0.219110 
   MLE     0.020756  |  0.008348 
  0.750    0.023245  | -0.219127 
  0.875    0.025235  | -0.653311 
  0.950    0.027541  | -1.344429 
  0.975    0.029154  | -1.912416 
  0.995    0.032670  | -3.309210 


===========================================================================
User Specified Options
===========================================================================

Force specific options:
-----------------------

Starting Parameters:

Theta (USR)                               0.010000



Search Strategy:
----------------

Type of analysis:  Likelihood

Number of replicates:  1

Markov Chain Parameters:
                           Initial           Final
  Number of Chains              10               2
     Trees Sampled              20              50
Sampling Increment              20              20
   Trees Discarded             100             100

Random number seed             1005                                    


File options:
-------------

Read data from file:           sample_infile.xml                       
Wrote summary file:            sample_outsumfile.xml                   
Wrote to Tracer file(s):       sample_tracefile_coal_1.txt             


Output summary options:
-----------------------

Calculate profile likelihoods? Yes                                     

===========================================================================
Data summary
===========================================================================

Number of populations:                                      1
Number of regions:                                          1
Total number of samples in all regions                     40


Region summary:
---------------

Population      Variable  Relative  Relative  Pairwise   Sample  
   Region       markers      Ne     rec rate   theta      size   
1 ZMNE
     1 coal        65        1        1.0    0.0152814     40    
-----------------------------------------------------------------


Summary of Data Model Parameters:
---------------------------------


---------------------------------------------------------------------------

Parameters of a Felsenstein '84 model for the #1 segment of the coal region
2 rate categories with correlated length 1
Relative rate 0.666669  Frequency 0.5
Relative rate 1.33333  Frequency 0.5
Base frequencies: 0.222692, 0.31, 0.163077, 0.304231
Transition/transversion ratio: 2
---------------------------------------------------------------------------

Input Genetic Data
---------------------------------------------------------------------------
   For the coal region
---------------------------------------------------------------------------
                                  #1                                  
00_0025   TGAAGCCCCAATTATGGTTACCACGACTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0032   TGAAGCCCCAATTATGGTTACCACGACTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0003   CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0022   CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0000   CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0024   CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0013   CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTAAGCGACGTGGGCTCTATCTCTCA
00_0027   CCACATCGTAGACGTTCGTGGCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTAA
00_0009   CCACATCGTAGACGTTCGTGCCGCTTCTTCTCAGTACCACTTAGCAACGTAGACTCTAACACTCA
00_0037   CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
00_0034   CCACATCGTAGACGTTCGTACCGCTTCCTCTCAGTACCACTTAGCAACGTAGACTCTATCACTCA
00_0038   CCACATCGTAGACGTTCGTACCGCTTCCTCTCAGTACCACTTAGCAACGTAGACTCTATCACTCA
00_0023   CCACATCGTAGACGTTCGTACCGCTTCCTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
00_0030   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
00_0002   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
00_0031   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
00_0014   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0018   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
00_0005   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0036   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0001   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0010   CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCCCA
00_0004   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0011   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0029   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0033   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0006   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0015   CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
00_0028   CCACATCGTTGACATTCGCACTGGTTTTCATTATTACCACATAGTGTCTCAGGTTCATTCTCTCA
00_0035   CCACATCGTTGACATTCGCACTGGTTTTCATTATTACCACATAGTGTCTCAGGTTCATTCTCTCA
00_0007   CCGCATCGTTGACATTCGCACTGGTTTTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
00_0026   CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
00_0019   CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
00_0020   CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
00_0016   CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATGGTGTATCAAGTTCATTCTCTCA
00_0021   CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
00_0017   CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGGCATATGGTGTATCAAGTTCATTCTCTCA
00_0039   CCACATTGTTGACATTCGCACTGGTTCTCATTAGCGCCATATAATGTATCAAGTTTATTCTCTCA
00_0008   CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTTTCG
00_0012   CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGCTATATAGTGTATCAAGTTCATTCTCTCG


===========================================================================
Run Reports by Region
===========================================================================

"Accepted" is the observed rate at which any change to the proposal trees
  was accepted.

11:48:08  Beginning region: coal
Initial Chain 1 of 10:
11:48:09  Predicted end of chains for this region:  Tue May 29 11:48:22 2012

11:48:09  Accepted    60% | Posterior lnL 1.90107653 | Data lnL -1531.22692
No trees discarded due to limit violations.
Haplotype-Arranger accepted       185/188 proposals
Tree-Arranger accepted             45/182 proposals
Tree-Size-Arranger accepted        10/30 proposals
  Theta       0.014005  
  
Initial Chain 2 of 10:
11:48:10  Predicted end of chains for this region:  Tue May 29 11:48:22 2012

11:48:10  Accepted    51% | Posterior lnL 2.00607272 | Data lnL -1223.59186
No trees discarded due to limit violations.
Haplotype-Arranger accepted       178/182 proposals
Tree-Arranger accepted             20/173 proposals
Tree-Size-Arranger accepted         6/45 proposals
  Theta       0.019801  
  
Initial Chain 3 of 10:
11:48:11  Predicted end of chains for this region:  Tue May 29 11:48:22 2012

11:48:11  Accepted    48% | Posterior lnL 0.31579072 | Data lnL -1144.89455
No trees discarded due to limit violations.
Haplotype-Arranger accepted       168/170 proposals
Tree-Arranger accepted             22/191 proposals
Tree-Size-Arranger accepted         2/39 proposals
  Theta       0.023710  
  
Initial Chain 4 of 10:
11:48:12  Predicted end of chains for this region:  Tue May 29 11:48:22 2012

11:48:12  Accepted 54.25% | Posterior lnL 0.06297012 | Data lnL -1045.63873
No trees discarded due to limit violations.
Haplotype-Arranger accepted       196/199 proposals
Tree-Arranger accepted             16/165 proposals
Tree-Size-Arranger accepted         5/36 proposals
  Theta       0.022223  
  
Initial Chain 5 of 10:
11:48:13  Predicted end of chains for this region:  Tue May 29 11:48:22 2012

11:48:13  Accepted  47.5% | Posterior lnL 0.14588871 | Data lnL -988.502230
No trees discarded due to limit violations.
Haplotype-Arranger accepted       173/178 proposals
Tree-Arranger accepted             14/197 proposals
Tree-Size-Arranger accepted         3/25 proposals
  Theta       0.024275  
  
Initial Chain 6 of 10:
11:48:13  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:13  Accepted 48.25% | Posterior lnL 0.00676027 | Data lnL -852.329277
No trees discarded due to limit violations.
Haplotype-Arranger accepted       165/166 proposals
Tree-Arranger accepted             23/196 proposals
Tree-Size-Arranger accepted         5/38 proposals
  Theta       0.023819  
  
Initial Chain 7 of 10:
11:48:14  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:14  Accepted 52.25% | Posterior lnL 0.01444143 | Data lnL -810.236477
No trees discarded due to limit violations.
Haplotype-Arranger accepted       192/197 proposals
Tree-Arranger accepted             11/172 proposals
Tree-Size-Arranger accepted         6/31 proposals
  Theta       0.023160  
  
Initial Chain 8 of 10:
11:48:15  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:15  Accepted  50.5% | Posterior lnL 0.09752478 | Data lnL -743.664624
No trees discarded due to limit violations.
Haplotype-Arranger accepted       187/188 proposals
Tree-Arranger accepted             14/191 proposals
Tree-Size-Arranger accepted         1/21 proposals
  Theta       0.021484  
  
Initial Chain 9 of 10:
11:48:16  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:16  Accepted 50.25% | Posterior lnL 0.01912259 | Data lnL -716.659601
No trees discarded due to limit violations.
Haplotype-Arranger accepted       180/181 proposals
Tree-Arranger accepted             19/185 proposals
Tree-Size-Arranger accepted         2/34 proposals
  Theta       0.022171  
  
Initial Chain 10 of 10:
11:48:17  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:17  Accepted    47% | Posterior lnL 0.01905120 | Data lnL -696.976981
No trees discarded due to limit violations.
Haplotype-Arranger accepted       173/173 proposals
Tree-Arranger accepted             14/186 proposals
Tree-Size-Arranger accepted         1/41 proposals
  Theta       0.021476  
  
Final Chain 1 of 2:
11:48:19  Predicted end of chains for this region:  Tue May 29 11:48:20 2012

11:48:19  Accepted    45% | Posterior lnL 0.05740946 | Data lnL -693.380385
No trees discarded due to limit violations.
Haplotype-Arranger accepted       422/423 proposals
Tree-Arranger accepted             28/483 proposals
Tree-Size-Arranger accepted         0/94 proposals
  Theta       0.020319  
  
Final Chain 2 of 2:
11:48:20  Accepted  47.6% | Posterior lnL 0.00834775 | Data lnL -687.920715
No trees discarded due to limit violations.
Haplotype-Arranger accepted       438/448 proposals
Tree-Arranger accepted             32/473 proposals
Tree-Size-Arranger accepted         6/79 proposals
  Theta       0.020756  
  
11:48:20  Beginning profiling, please be patient
11:48:20  Finished profile 1 of 1.


