--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu May 10 16:41:59 WEST 2018 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS1/DNG_N2/NS2B_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -3539.22 -3590.13 2 -3543.61 -3585.44 -------------------------------------- TOTAL -3539.90 -3589.44 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 7.522369 0.330064 6.445980 8.689019 7.503303 1069.88 1102.57 1.000 r(A<->C){all} 0.059563 0.000169 0.035817 0.085609 0.058660 751.82 813.96 1.001 r(A<->G){all} 0.256235 0.000712 0.200860 0.305538 0.256005 478.48 554.40 1.000 r(A<->T){all} 0.088500 0.000197 0.059575 0.114151 0.087793 862.16 987.45 1.000 r(C<->G){all} 0.064357 0.000186 0.040182 0.093395 0.063934 656.21 755.86 1.000 r(C<->T){all} 0.522927 0.001035 0.464147 0.588314 0.522538 474.07 571.10 1.000 r(G<->T){all} 0.008418 0.000043 0.000006 0.021095 0.007029 881.07 915.15 1.002 pi(A){all} 0.325580 0.000247 0.295965 0.356686 0.325172 1062.48 1107.07 1.000 pi(C){all} 0.216695 0.000189 0.189690 0.243669 0.216382 858.19 968.75 1.000 pi(G){all} 0.237463 0.000212 0.209627 0.265927 0.237399 691.55 789.41 1.000 pi(T){all} 0.220262 0.000191 0.192226 0.246337 0.220087 697.15 816.62 1.000 alpha{1,2} 0.224549 0.000667 0.174714 0.274691 0.222906 1287.87 1333.52 1.000 alpha{3} 3.996541 0.884805 2.303337 5.823713 3.898486 1476.21 1488.61 1.000 pinvar{all} 0.051378 0.000565 0.008576 0.098992 0.049857 1380.00 1440.50 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -3176.572722 Model 2: PositiveSelection -3176.572722 Model 0: one-ratio -3179.853132 Model 3: discrete -3158.121053 Model 7: beta -3159.055428 Model 8: beta&w>1 -3159.052072 Model 0 vs 1 6.560820000000604 Model 2 vs 1 0.0 Model 8 vs 7 0.006712000000334228
>C1 SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK LALITVSGLYPLAIPVTMALWYIWQVKTQR >C2 SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD LTVEKAADITWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK TALLIVSGIFPYSIPATLLVWHTWQKQTQR >C3 SWPLNEGIMAVGVVSILLSSLLKDDVPLAGPLIAGGMLIACYVISGSSAD LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK ATLLAVSGVYPLSIPATLFVWYFWQKKKQR >C4 SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD LSLEKAAVVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK ATLLAVSGVYPLSIPATLFVWYFWQKKKQR >C5 SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD LELERAADVRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR TGLLVISGLFPVSIPITAAAWYLWEVKKQR >C6 SWPLNEAVMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD LELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEHTLTILIR TGLLVISGVFPVSIPITAAAWYLWEVKKQR >C7 SWPLNEoVMAVoLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD LTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK TALLIVSGIFPYSIPATLLVWHTWQKQTQR >C8 SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD LSLEKAAEVSWEDEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK ATLLVISGV