************************************************************ LAMARC: Maximum Likelihood Parameter Estimation using Hastings-Metropolis Markov Chain Monte Carlo ************************************************************ version 2.1 Program started on Mon Apr 16 13:12:40 2007 finished on Mon Apr 16 14:19:18 2007 =========================================================================== Maximum Likelihood Estimates (MLEs) of Parameters =========================================================================== Theta Population Theta1 Best Val (MLE) 0.111759 Percentile 99% 0.005 0.067041 95% 0.025 0.075329 90% 0.050 0.080063 75% 0.125 0.088263 50% 0.250 0.097161 MLE 0.111759 50% 0.750 0.129156 75% 0.875 0.143464 90% 0.950 0.160461 95% 0.975 0.172597 99% 0.995 0.199759 Theta1: Theta for pop1 Rec RecRate Best Val (MLE) 0.055332 Percentile 99% 0.005 0.021823 95% 0.025 0.027856 90% 0.050 0.031392 75% 0.125 0.037593 50% 0.250 0.044352 MLE 0.055332 50% 0.750 0.068047 75% 0.875 0.078105 90% 0.950 0.089509 95% 0.975 0.097263 99% 0.995 0.113430 Rec: Recombination Rate =========================================================================== Profile Likelihoods =========================================================================== The first listed parameter is the parameter held constant. =========================================================================== Overall Profile Tables =========================================================================== Overall: Theta for pop1 (Theta1): --------------------------------- Log Likelihoods: Percentile Theta1 | Ln(L) 0.005 0.067041 | -3.304230 0.025 0.075329 | -1.907465 0.050 0.080063 | -1.339487 0.125 0.088263 | -0.648331 0.250 0.097161 | -0.214158 MLE 0.111759 | 0.013301 0.750 0.129156 | -0.214156 0.875 0.143464 | -0.648340 0.950 0.160461 | -1.339487 0.975 0.172597 | -1.907457 0.995 0.199759 | -3.304203 Best fit parameters with Theta1 held constant: Percentile Theta1 | Rec 0.005 0.067041 | 0.058722 0.025 0.075329 | 0.058200 0.050 0.080063 | 0.057868 0.125 0.088263 | 0.057247 0.250 0.097161 | 0.056535 MLE 0.111759 | 0.055332 0.750 0.129156 | 0.053929 0.875 0.143464 | 0.052847 0.950 0.160461 | 0.051670 0.975 0.172597 | 0.050902 0.995 0.199759 | 0.049399 Overall: RecRate (Rec): ----------------------- Log Likelihoods: Percentile Rec | Ln(L) 0.005 0.021823 | -3.304223 0.025 0.027856 | -1.907460 0.050 0.031392 | -1.339469 0.125 0.037593 | -0.648360 0.250 0.044352 | -0.214172 MLE 0.055332 | 0.013301 0.750 0.068047 | -0.214175 0.875 0.078105 | -0.648363 0.950 0.089509 | -1.339498 0.975 0.097263 | -1.907456 0.995 0.113430 | -3.304205 =========================================================================== Profile Likelihoods (cont.) (overall profile tables) =========================================================================== Best fit parameters with Rec held constant: Percentile Rec | Theta1 0.005 0.021823 | 0.117712 0.025 0.027856 | 0.116560 0.050 0.031392 | 0.115875 0.125 0.037593 | 0.114706 0.250 0.044352 | 0.113511 MLE 0.055332 | 0.111759 0.750 0.068047 | 0.110041 0.875 0.078105 | 0.108958 0.950 0.089509 | 0.108052 0.975 0.097263 | 0.107618 0.995 0.113430 | 0.107071 =========================================================================== 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: 837:841. Relative data likelihood = 0.00219225 The top 5% of all sites in this region: 824:841, 879:883 The top 50% of all sites in this region: 673:737, 824:988 The top 95% of all sites in this region: 1:213, 232:233, 638:988 You have a total of 566 sites in your 95% range. Site Data likelihood 1 0.00069191 2 0.00069390 3 0.00070106 4 0.00070132 5 0.00070553 6 0.00070598 7 0.00071026 8 0.00070982 9 0.00070983 10 0.00071138 11 0.00071155 12 0.00071162 13 0.00071315 14 0.00071315 15 0.00086100 16 0.00086963 17 0.00087915 18 0.00087915 19 0.00087904 20 0.00087876 21 0.00087876 22 0.00088050 23 0.00088185 24 0.00088185 25 0.00088185 26 0.00089291 27 0.00089727 28 0.00089715 29 0.00089715 30 0.00092756 31 0.00092814 32 0.00096198 33 0.00096198 34 0.00097710 35 0.00097694 36 0.00097694 37 0.00097719 38 0.00097719 39 0.00097719 40 0.00097719 41 0.00097719 42 0.00097716 43 0.00097753 44 0.00097753 45 0.00097725 46 0.00097727 47 0.00097724 48 0.00097724 49 0.00097717 50 0.00097717 51 0.00096236 52 0.00096236 53 0.00096236 54 0.00096236 55 0.00096233 56 0.00096242 57 0.00096242 58 0.00096215 59 0.00096178 60 0.00096283 61 0.00096286 62 0.00096286 63 0.00096179 64 0.00096096 65 0.00096091 66 0.00096102 67 0.00096102 68 0.00096157 69 0.00096167 70 0.00096165 71 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=========================================================================== 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 1176754361 File options: ------------- Read data from file: lamarc-trait-input.xml Wrote to trace 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. 13:12:42 Beginning region: region1 Initial Chain 1 of 10: 13:13:10 Predicted end of chains for this region: Mon Apr 16 13:34:25 2007 13:13:10 Accepted 5.19% | Posterior lnL 23.0866791 | Data lnL -3427.50715 No trees discarded due to limit violations. Tree-Arranger accepted 383/8332 proposals Tree-Size-Arranger accepted 136/1668 proposals Theta 0.038309 Rec 0.016683 Initial Chain 2 of 10: 13:13:41 Predicted end of chains for this region: Mon Apr 16 13:35:35 2007 13:13:41 Accepted 7.2% | Posterior lnL 8.94281007 | Data lnL -3252.00987 No trees discarded due to limit violations. Tree-Arranger accepted 535/8346 proposals Tree-Size-Arranger accepted 185/1654 proposals Theta 0.090801 Rec 0.019059 Initial Chain 3 of 10: 13:14:13 Predicted end of chains for this region: Mon Apr 16 13:36:13 2007 13:14:13 Accepted 4.56% | Posterior lnL 0.46997038 | Data lnL -3233.96354 No trees discarded due to limit violations. Tree-Arranger accepted 348/8281 proposals Tree-Size-Arranger accepted 108/1719 proposals Theta 0.112708 Rec 0.019398 Initial Chain 4 of 10: 13:14:48 Predicted end of chains for this region: Mon Apr 16 13:37:08 2007 13:14:48 Accepted 4.98% | Posterior lnL 0.18604850 | Data lnL -3225.25334 No trees discarded due to limit violations. Tree-Arranger accepted 387/8326 proposals Tree-Size-Arranger accepted 111/1674 proposals Theta 0.124086 Rec 0.023064 Initial Chain 5 of 10: 13:15:22 Predicted end of chains for this region: Mon Apr 16 13:37:31 2007 13:15:22 Accepted 4.97% | Posterior lnL 0.15513192 | Data lnL -3229.79119 No trees discarded due to limit violations. Tree-Arranger accepted 397/8404 proposals Tree-Size-Arranger accepted 100/1596 proposals Theta 0.116830 Rec 0.028129 Initial Chain 6 of 10: 13:15:57 Predicted end of chains for this region: Mon Apr 16 13:37:54 2007 13:15:57 Accepted 5.19% | Posterior lnL 0.03719715 | Data lnL -3208.84594 No trees discarded due to limit violations. Tree-Arranger accepted 383/8277 proposals Tree-Size-Arranger accepted 136/1723 proposals Theta 0.112742 Rec 0.031319 Initial Chain 7 of 10: 13:16:34 Predicted end of chains for this region: Mon Apr 16 13:38:24 2007 13:16:34 Accepted 7.28% | Posterior lnL 0.01478876 | Data lnL -3193.29923 No trees discarded due to limit violations. Tree-Arranger accepted 541/8292 proposals Tree-Size-Arranger accepted 187/1708 proposals Theta 0.114950 Rec 0.033197 Initial Chain 8 of 10: 13:17:13 Predicted end of chains for this region: Mon Apr 16 13:38:58 2007 13:17:13 Accepted 6.34% | Posterior lnL 0.30933274 | Data lnL -3165.21480 No trees discarded due to limit violations. Tree-Arranger accepted 511/8342 proposals Tree-Size-Arranger accepted 123/1658 proposals Theta 0.109936 Rec 0.046501 Initial Chain 9 of 10: 13:17:57 Predicted end of chains for this region: Mon Apr 16 13:39:51 2007 13:17:57 Accepted 7.61% | Posterior lnL 0.07880569 | Data lnL -3162.84028 No trees discarded due to limit violations. Tree-Arranger accepted 562/8383 proposals Tree-Size-Arranger accepted 199/1617 proposals Theta 0.118914 Rec 0.047440 Initial Chain 10 of 10: 13:18:43 Predicted end of chains for this region: Mon Apr 16 13:40:42 2007 13:18:43 Accepted 6.88% | Posterior lnL 0.20222578 | Data lnL -3161.99407 No trees discarded due to limit violations. Tree-Arranger accepted 515/8388 proposals Tree-Size-Arranger accepted 173/1612 proposals Theta 0.108950 Rec 0.054666 Final Chain 1 of 2: 13:33:46 Predicted end of chains for this region: Mon Apr 16 13:47:22 2007 13:33:46 Accepted 8.364% | Posterior lnL 0.03290702 | Data lnL -3135.34101 No trees discarded due to limit violations. Tree-Arranger accepted 11855/166744 proposals Tree-Size-Arranger accepted 4874/33256 proposals Theta 0.112721 Rec 0.058050 Final Chain 2 of 2: 13:50:09 Accepted 8.226% | Posterior lnL 0.01330102 | Data lnL -3121.43541 No trees discarded due to limit violations. Tree-Arranger accepted 11803/166349 proposals Tree-Size-Arranger accepted 4650/33651 proposals Theta 0.111759 Rec 0.055332 13:50:09 Most likely site(s) for funny-nose: 837:841. Relative data likelihood = 0.00219225 The top 5% of all sites in this region: 824:841, 879:883 The top 50% of all sites in this region: 673:737, 824:988 The top 95% of all sites in this region: 1:213, 232:233, 638:988 You have a total of 566 sites in your 95% range. 13:50:09 Beginning profiling, please be patient 14:00:30 Finished profile 1 of 2. Predicted end of this set of profiles: Mon Apr 16 14:10:51 2007 14:19:18 Finished profile 2 of 2.