Analyses for Study

Analyses

Analysis 1

Analysis details

Input data 1 Input object(s) Micropontica mt

Analysis step Micropontica BI -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands begin mrbayes; [Define character sets] charset 1st2nd = 2 - 655\3 3 - 655\3; charset 3rd = 1 - 655\3; charset 16S = 656 - 1126; [Define partition] partition gene_partition = 3: 1st2nd, 3rd, 16S; exclude 667 - 672 702 - 703 810 850 - 851 896 - 897 906 912 951 - 952 966 - 968 991 - 992; [Select partition] set partition = gene_partition; [Selects model for partition 1st] lset applyto = (1) nst=6 rates=invgamma; [Selects model for partition 3rd] lset applyto = (2) nst=6 rates=gamma; [Selects model for partition 16S] lset applyto = (3) nst=6 rates=gamma; [Unlink parameters across partitions] unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all); [Allow rates to vary across all partitions] prset ratepr = variable; mcmcp ngen=5000000 printfreq=1000 samplefreq=1000 nruns=2 nchains=4 savebrlens=yes printall=yes mcmcdiagn=yes diagnfreq=10000 relburnin=no;

Output data 1 Output object(s) con 50 majrule

Analysis 2

Analysis details

Input data 1 Input object(s) Micropontica mt

Analysis step Micropontica ML -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands begin sets; [Define character sets] charset 1st2nd = 2 - 655\3 3 - 655\3; charset 3rd = 1 - 655\3; charset 16S = 656 - 1126; [Define partition] charpartition gene_partition = COI1st2nd:1st2nd, COI3rd:3rd, 16SrRNA:16S; exset * 16Sgblocksexcluded = 667 - 672 702 - 703 810 850 - 851 896 - 897 906 912 951 - 952 966 - 968 991 - 992; end; [model1] datatype = nucleotide ratematrix = (a b c c e a) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = ( a b c c e a ) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [model3] datatype = nucleotide ratematrix = ( a b c d e f ) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none

Output data 1 Output object(s) rep5BEST