Analyses for Study

Analyses

Analysis 1

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids ASF-updated

Analysis step Heuristic Search -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [treesearch] hsearch swap=tbr addseq=random nreps=100; set increase=auto autoinc=100;

Output data 5 Output object(s) ASF-like MP 1 ASF-like MP 2 ASF-like MP 3 ASF-like MP 4 ASF-like MP 5

Input data 1 Input object(s) Phytophthora hybrids ASF-updated

Analysis step Bootstrap analysis -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [bootstrap] set increase=auto autoinc=100; bootstrap nreps=1000;

Output data 1 Output object(s) ASF-like MP bootstrap

Analysis 2

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids ASF-updated

Analysis step Bayesian Inference -- 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; Prset statefreqpr=dirichlet(1111); Lset nst=6 rates=gamma; mcmcp ngen=5000000

Output data 1 Output object(s) ASF-like Bayesian inference

Analysis 3

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids GPA

Analysis step Heuristic Search -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [treesearch] hsearch swap=tbr addseq=random nreps=100; set increase=auto autoinc=100;

Output data 4 Output object(s) GPA1 MP 1 GPA1 MP 2 GPA1 MP 3 GPA1 MP 4

Input data 1 Input object(s) Phytophthora hybrids GPA

Analysis step Bootstrap analysis -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [bootstrap] set increase=auto autoinc=100; bootstrap nreps=1000;

Output data 1 Output object(s) GPA1 MP bootstrap consensus

Analysis 4

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids GPA

Analysis step Bayesian Inference -- 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; Prset statefreqpr=dirichlet(1111); Lset nst=6 rates=gamma; mcmcp ngen=5000000

Output data 1 Output object(s) GPA1 Bayesian inference

Analysis 5

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids COX

Analysis step Heuristic Search -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [treesearch] hsearch swap=tbr addseq=random nreps=100; set increase=auto autoinc=100;

Output data 1 Output object(s) coxI MP 1

Input data 1 Input object(s) Phytophthora hybrids COX

Analysis step Bootstrap analysis -- Step details Name Software used Name Version Algorithm --- Please Select --- maximum likelihood parsimony bayesian inference minimum evolution neighbor joining UPGMA other algorithm Commands [bootstrap] set increase=auto autoinc=100; bootstrap nreps=1000;

Output data 1 Output object(s) coxI MP bootstrap consensus

Analysis 6

Analysis details

Name

Input data 1 Input object(s) Phytophthora hybrids COX

Analysis step Bayesian Inference -- 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; Prset statefreqpr=dirichlet(1111); Lset nst=6 rates=invgamma; mcmcp ngen=5000000

Output data 1 Output object(s) CoxI Bayesian inference