************************************************************ LAMARC: Maximum Likelihood Parameter Estimation using Hastings-Metropolis Markov Chain Monte Carlo ************************************************************ version 2.1.3 Program started on Fri Jul 11 15:04:05 2008 finished on Fri Jul 11 16:20:32 2008 =========================================================================== Maximum Likelihood Estimates (MLEs) of Parameters =========================================================================== Theta Population Theta1 Best Val (MLE) 0.120621 Percentile 99% 0.005 0.071116 95% 0.025 0.080300 90% 0.050 0.085565 75% 0.125 0.094684 50% 0.250 0.104548 MLE 0.120621 50% 0.750 0.139607 75% 0.875 0.155109 90% 0.950 0.173419 95% 0.975 0.186433 99% 0.995 0.215416 Theta1: Theta for pop1 Rec RecRate Best Val (MLE) 0.054609 Percentile 99% 0.005 0.022539 95% 0.025 0.028421 90% 0.050 0.031831 75% 0.125 0.037767 50% 0.250 0.044197 MLE 0.054609 50% 0.750 0.066650 75% 0.875 0.076151 90% 0.950 0.086889 95% 0.975 0.094172 99% 0.995 0.109338 Rec: Recombination Rate =========================================================================== Profile Likelihoods =========================================================================== The first listed parameter is the parameter held constant. =========================================================================== Overall Profile Tables =========================================================================== Overall: Theta for pop1 (Theta1): --------------------------------- Percentile profile: Points shown indicate approximate confidence intervals. Log Likelihoods: Percentile Theta1 | Ln(L) 0.005 0.071116 | -3.219535 0.025 0.080300 | -1.822809 0.050 0.085565 | -1.254813 0.125 0.094684 | -0.563671 0.250 0.104548 | -0.129503 MLE 0.120621 | 0.097962 0.750 0.139607 | -0.129520 0.875 0.155109 | -0.563700 0.950 0.173419 | -1.254805 0.975 0.186433 | -1.822791 0.995 0.215416 | -3.219533 Best fit parameters with Theta1 held constant: Percentile Theta1 | Rec 0.005 0.071116 | 0.060394 0.025 0.080300 | 0.059115 0.050 0.085565 | 0.058371 0.125 0.094684 | 0.057177 0.250 0.104548 | 0.056067 MLE 0.120621 | 0.054609 0.750 0.139607 | 0.053246 0.875 0.155109 | 0.052318 0.950 0.173419 | 0.051384 0.975 0.186433 | 0.050810 0.995 0.215416 | 0.049755 =========================================================================== Profile Likelihoods (cont.) (overall profile tables) =========================================================================== Overall: RecRate (Rec): ----------------------- Percentile profile: Points shown indicate approximate confidence intervals. Log Likelihoods: Percentile Rec | Ln(L) 0.005 0.022539 | -3.219546 0.025 0.028421 | -1.822793 0.050 0.031831 | -1.254816 0.125 0.037767 | -0.563699 0.250 0.044197 | -0.129513 MLE 0.054609 | 0.097962 0.750 0.066650 | -0.129509 0.875 0.076151 | -0.563680 0.950 0.086889 | -1.254805 0.975 0.094172 | -1.822802 0.995 0.109338 | -3.219510 Best fit parameters with Rec held constant: Percentile Rec | Theta1 0.005 0.022539 | 0.126765 0.025 0.028421 | 0.125720 0.050 0.031831 | 0.125087 0.125 0.037767 | 0.123945 0.250 0.044197 | 0.122676 MLE 0.054609 | 0.120621 0.750 0.066650 | 0.118366 0.875 0.076151 | 0.116735 0.950 0.086889 | 0.115070 0.975 0.094172 | 0.114053 0.995 0.109338 | 0.112237 =========================================================================== Mapping results =========================================================================== This analysis for this trait was performed by collecting trees, then calculating the data likelihood of the trait marker at all allowed sites on those trees, and then averaging. Mapping results for funny-nose from the region "region1". Most likely site(s) for funny-nose: 919:923. Relative data likelihood = 0.0025891 The top 5% of all sites in this region: 919:936, 946:947 The top 50% of all sites in this region: 678:709, 776:803, 811:953 The top 95% of all sites in this region: 1:212, 214:215, 217:220, 641:953 You have a total of 531 sites in your 95% range. =========================================================================== User Specified Options =========================================================================== Force specific options: ----------------------- Starting Parameters: Search Strategy: ---------------- Type of analysis: Likelihood Number of replicates: 1 Markov Chain Parameters: Initial Final Number of Chains 10 2 Trees Sampled 500 10000 Sampling Increment 20 20 Trees Discarded 1000 1000 Random number seed 1215813845 File options: ------------- Read data from file: lamarc-trait-input.xml Wrote to mapping file(s): mapfile_funny-nose.txt Wrote to Tracer file(s): tracefile_region1_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 16 Linked-segments by region: -------------------------- Datatype MuRate region1 | | #1 | DNA 1 |funny-nose K-Allele 1 --------------------------------------------------------- Region summary: --------------- Population Variable Relative Relative Pairwise Sample Region markers Ne rec rate theta size 1 pop1 1 region1 232 1 1.0 0.0699168 16 ----------------------------------------------------------------- Summary of Data Model Parameters: --------------------------------- --------------------------------------------------------------------------- Parameters of a Felsenstein '84 model for the #1 segment of the region1 region Base frequencies: 0.255625, 0.254875, 0.217562, 0.271937 Transition/transversion ratio: 2 --------------------------------------------------------------------------- Parameters of a K Allele model for the funny-nose segment of the region1 region Maximum number of bins: 2 --------------------------------------------------------------------------- =========================================================================== Run Reports by Region =========================================================================== "Accepted" is the observed rate at which any change to the proposal trees was accepted. 15:04:07 Beginning region: region1 Initial Chain 1 of 10: 15:04:37 Predicted end of chains for this region: Fri Jul 11 15:27:23 2008 15:04:37 Accepted 4.94% | Posterior lnL 32.1234746 | Data lnL -3410.96008 No trees discarded due to limit violations. Tree-Arranger accepted 427/8302 proposals Tree-Size-Arranger accepted 67/1698 proposals Theta 0.040525 Rec 0.034930 Initial Chain 2 of 10: 15:05:12 Predicted end of chains for this region: Fri Jul 11 15:29:19 2008 15:05:12 Accepted 10.73% | Posterior lnL 8.30673609 | Data lnL -3253.77947 No trees discarded due to limit violations. Tree-Arranger accepted 755/8335 proposals Tree-Size-Arranger accepted 318/1665 proposals Theta 0.094397 Rec 0.036964 Initial Chain 3 of 10: 15:05:51 Predicted end of chains for this region: Fri Jul 11 15:31:00 2008 15:05:51 Accepted 8.28% | Posterior lnL 0.48837554 | Data lnL -3210.75409 No trees discarded due to limit violations. Tree-Arranger accepted 621/8313 proposals Tree-Size-Arranger accepted 207/1687 proposals Theta 0.116520 Rec 0.031698 Initial Chain 4 of 10: 15:06:33 Predicted end of chains for this region: Fri Jul 11 15:32:25 2008 15:06:33 Accepted 7.4% | Posterior lnL 0.11244487 | Data lnL -3212.79690 No trees discarded due to limit violations. Tree-Arranger accepted 600/8328 proposals Tree-Size-Arranger accepted 140/1672 proposals Theta 0.117805 Rec 0.037398 Initial Chain 5 of 10: 15:07:13 Predicted end of chains for this region: Fri Jul 11 15:32:58 2008 15:07:13 Accepted 7.88% | Posterior lnL 0.07669565 | Data lnL -3209.77447 No trees discarded due to limit violations. Tree-Arranger accepted 650/8414 proposals Tree-Size-Arranger accepted 138/1586 proposals Theta 0.114143 Rec 0.042701 Initial Chain 6 of 10: 15:07:56 Predicted end of chains for this region: Fri Jul 11 15:33:43 2008 15:07:56 Accepted 7.15% | Posterior lnL 0.13397531 | Data lnL -3188.94408 No trees discarded due to limit violations. Tree-Arranger accepted 510/8330 proposals Tree-Size-Arranger accepted 205/1670 proposals Theta 0.125161 Rec 0.037918 Initial Chain 7 of 10: 15:08:48 Predicted end of chains for this region: Fri Jul 11 15:35:15 2008 15:08:48 Accepted 7.19% | Posterior lnL 1.32304194 | Data lnL -3158.82103 No trees discarded due to limit violations. Tree-Arranger accepted 588/8350 proposals Tree-Size-Arranger accepted 131/1650 proposals Theta 0.117245 Rec 0.061214 Initial Chain 8 of 10: 15:09:43 Predicted end of chains for this region: Fri Jul 11 15:36:41 2008 15:09:43 Accepted 8.92% | Posterior lnL 0.12144198 | Data lnL -3155.91152 No trees discarded due to limit violations. Tree-Arranger accepted 682/8318 proposals Tree-Size-Arranger accepted 210/1682 proposals Theta 0.112106 Rec 0.069393 Initial Chain 9 of 10: 15:10:39 Predicted end of chains for this region: Fri Jul 11 15:37:54 2008 15:10:39 Accepted 9.88% | Posterior lnL 0.05952281 | Data lnL -3149.13796 No trees discarded due to limit violations. Tree-Arranger accepted 662/8316 proposals Tree-Size-Arranger accepted 326/1684 proposals Theta 0.120211 Rec 0.068023 Initial Chain 10 of 10: 15:11:33 Predicted end of chains for this region: Fri Jul 11 15:38:42 2008 15:11:33 Accepted 9.41% | Posterior lnL 0.27065307 | Data lnL -3139.63750 No trees discarded due to limit violations. Tree-Arranger accepted 616/8323 proposals Tree-Size-Arranger accepted 325/1677 proposals Theta 0.105426 Rec 0.076304 Final Chain 1 of 2: 15:28:09 Predicted end of chains for this region: Fri Jul 11 15:43:40 2008 15:28:09 Accepted 9.998% | Posterior lnL 0.33009443 | Data lnL -3125.44391 No trees discarded due to limit violations. Tree-Arranger accepted 13481/166785 proposals Tree-Size-Arranger accepted 6516/33215 proposals Theta 0.113947 Rec 0.061273 Final Chain 2 of 2: 15:44:03 Accepted 8.22% | Posterior lnL 0.09796165 | Data lnL -3121.52779 No trees discarded due to limit violations. Tree-Arranger accepted 11251/166512 proposals Tree-Size-Arranger accepted 5189/33488 proposals Theta 0.120621 Rec 0.054609 15:44:03 Most likely site(s) for funny-nose: 919:923. Relative data likelihood = 0.0025891 The top 5% of all sites in this region: 919:936, 946:947 The top 50% of all sites in this region: 678:709, 776:803, 811:953 The top 95% of all sites in this region: 1:212, 214:215, 217:220, 641:953 You have a total of 531 sites in your 95% range. 15:44:03 Beginning profiling, please be patient 16:01:59 Finished profile 1 of 2. Predicted end of this set of profiles: Fri Jul 11 16:19:55 2008 16:20:32 Finished profile 2 of 2.