Analyses for Study 11178

Analyses

Analysis 1

Analysis details

Name

Input data 1 Input object(s) atp1

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) atp1 BS PAUP 1

Analysis 2

Analysis details

Name

Input data 1 Input object(s) atp1

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-960; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=invgamma; mcmcp samplefreq=1000 ngen=5000000 filename=mb_atp1_0912.nex nruns=2 nchains=4;

Output data 1 Output object(s) atp1 MB con 50 majrule

Analysis 3

Analysis details

Name

Input data 1 Input object(s) cox3

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) COX3 BS PAUP 1

Analysis 4

Analysis details

Name

Input data 1 Input object(s) cox3

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-674; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=invgamma; mcmcp samplefreq=1000 ngen=5000000 filename=mb_cox3_0912.nex nruns=2 nchains=4;

Output data 1 Output object(s) COX3 MB con 50 majrule

Analysis 5

Analysis details

Name

Input data 1 Input object(s) nad9

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) nad9 BS PAUP 1

Analysis 6

Analysis details

Name

Input data 1 Input object(s) nad9

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-464; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=gamma; mcmcp samplefreq=1000 ngen=5000000 filename=mb_nad9_0912.nex nruns=2 nchains=4; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 2 Output object(s) nad9 MB con 50 majrule nad9 MB con 50 majrule

Analysis 7

Analysis details

Name

Input data 1 Input object(s) mtDNA

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) mtDNA BS PAUP 1

Analysis 8

Analysis details

Name

Input data 1 Input object(s) mtDNA

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-2099; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=invgamma; mcmcp samplefreq=1000 ngen=5000000 filename=mb_mtDNA_0912.nex nruns=2 nchains=4; mcmc;

Output data 1 Output object(s) mtDNA MB con 50 majrule

Analysis 9

Analysis details

Name

Input data 2 Input object(s) matK dna matK indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) matK BS PAUP 1

Analysis 10

Analysis details

Name

Input data 2 Input object(s) matK dna matK indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-1708; charset indels = 1709-.; [xx stycken] prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp ngen=5000000 printfreq=1000 samplefreq=1000 nchains=4 nruns=2 filename=mb_matK_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) matK MB con 50 majrule

Analysis 11

Analysis details

Name

Input data 2 Input object(s) rps16 dna rps16 indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) rps16 BS PAUP 1

Analysis 12

Analysis details

Name

Input data 2 Input object(s) rps16 dna rps16 indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-966; charset indels = 967-.; [xx stycken] prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp ngen=5000000 printfreq=1000 samplefreq=1000 nchains=4 nruns=2 filename=mb_rps16_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) rps16 MB con 50 majrule

Analysis 13

Analysis details

Name

Input data 2 Input object(s) trnLF dna trnLF indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands exclude 378-392 433-534 1126-1157 1468-1475 1482-1523 1590-1601; bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) trnLF BS PAUP 1

Analysis 14

Analysis details

Name

Input data 2 Input object(s) trnLF dna trnLF indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-1421; charset indels = 1422-.; exclude 378-392 433-534 1126-1157 1468-1475 1482-1523 1590-1601; partition type = 2:dna,indels; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp ngen=5000000 printfreq=1000 samplefreq=1000 nchains=4 nruns=2 filename=mb_trnLF_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) trnLF MB con 50 majrule

Analysis 15

Analysis details

Name

Input data 2 Input object(s) cpDNA dna cpDNA indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands exclude 3050-3064 3105-3206 3673-3703 4236-4243 4250-4291 4344-4347; bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) PAUP 1

Analysis 16

Analysis details

Name

Input data 2 Input object(s) cpDNA dna cpDNA indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-4092; charset indels = 4093-.; exclude 3050-3064 3105-3206 3673-3703 4236-4243 4250-4291 4344-4347; partition type = 2:dna,indels; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=invgamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nruns=2 nchains=4 filename=mb_cpDNA_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) cpDNA MB con 50 majrule

Analysis 17

Analysis details

Name

Input data 2 Input object(s) RPA2 dna RPA2 indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands exclude 865-883 1339-1369 2549-2559 2589-2610; bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) RPA2 PAUP 1

Analysis 18

Analysis details

Name

Input data 2 Input object(s) RPA2 dna RPA2 indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands charset dna = 1-2533; charset indels = 2534-.; [xx stycken] exclude 865-883 1339-1369 2549-2559 2589-2610; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nruns=2 nchains=4 filename=mb_RPA2_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) RPA2 mb con 50 majrule

Analysis 19

Analysis details

Name

Input data 2 Input object(s) RPB2 dna RPB2 indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands exclude 158-170 1016-1027; bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) PAUP 1

Analysis 20

Analysis details

Name

Input data 2 Input object(s) RPB2 dna RPB2 indels

Analysis step Untitled -- Software used Name Commands charset dna = 1-997; charset indels = 998-.; [xx stycken] exclude 158-170 1016-1027; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nruns=2 nchains=4 filename=mb_RPB2_con1009_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) con 50 majrule

Analysis 21

Analysis details

Name

Input data 2 Input object(s) RPD2a dna RPD2a indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) RPD2a BS PAUP 1

Analysis 22

Analysis details

Name

Input data 2 Input object(s) RPD2a dna RPD2a indels

Analysis step Untitled -- Software used Name Commands charset dna = 1-2013; charset indels = 2014-.; [xx stycken] prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nchains=4 filename=mb_RPD2a_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) RPD2a MB con 50 majrule

Analysis 23

Analysis details

Name

Input data 2 Input object(s) RPD2b dna RPD2b indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands exclude 18-32 763-770; bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) RPD2b BS PAUP 1

Analysis 24

Analysis details

Name

Input data 2 Input object(s) RPD2b dna RPD2b indels

Analysis step Untitled -- Software used Name Commands charset dna = 1-758; charset indels = 759-.; [xx stycken] exclude 18-32 763-770; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); lset applyto=(1) nst=6 rates=gamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nruns=2 nchains=4 filename=mb_RPD2b_con1010_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 1 Output object(s) RPD2b MB con 50 majrule

Analysis 25

Analysis details

Name

Input data 2 Input object(s) ITS dna ITS indels

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands bootstrap nreps=1000 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq hold=1 swap=tbr multrees=no;

Output data 1 Output object(s) ITS indels BS PAUP 1

Analysis 26

Analysis details

Name

Input data 2 Input object(s) ITS dna ITS indels

Analysis step Untitled -- Software used Name Commands charset dna = 1-853; charset indels = 854-.; [xx stycken] partition dna = 2:dna,indels; set partition=dna; prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); Lset applyto=(1) nst=6 rates=invgamma; prset applyto=(2) ratepr=variable; lset applyto=(2) rates=gamma; mcmcp samplefreq=1000 ngen=5000000 nruns=2 nchains=4 filename=mb_ITS_con1009_sic.nex; mcmc; sump burnin=1250 printtofile=yes; sumt burnin=1250;

Output data 2 Output object(s) ITS indels MB con 50 majrule ITS indels MB con 50 majrule

Analysis 27

Analysis details

Name

Input data 4 Input object(s) cpDNA LychnisSilene RPA2 LychnisSilene RPD2a LychnisSilene RPD2b LychnisSilene

Analysis step Untitled -- Software used Name Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm

Output data 4 Output object(s) FourGenes.cpDNA MCC.TREE1 FourGenes.d2a MCC.TREE1 FourGenes.d2b MCC.TREE1 FourGenes.RPA2 MCC.TREE1