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Analyses for Study 22552

Citation title: "Cryptic species diversity in polypores: the Skeletocutis nivea species complex".

Study name: "Cryptic species diversity in polypores: the Skeletocutis nivea species complex".

This study is part of submission 22552 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ML analysis of the Skeletocutis nivea species complex and outgroup taxa, nrRNA (ITS and LSU) dataset --

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

BI analysis of the Skeletocutis nivea species complex and outgroup taxa, nrRNA (ITS and LSU) dataset --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN MrBayes; log start filename=outgroup_ITS&LSU_CIPRES_Bayes.txt; set autoclose=yes; outgroup KY948740_Tyromyces_merulinus_ITS_LSU; CharSet ITS1et2 = 1-215 370-575; CharSet 5_8SetLSU = 216-369 576-2035; partition parts = 2: ITS1et2, 5_8SetLSU; set partition = parts; lset applyto=(1) nst=6 rates=gamma; lset applyto=(2) nst=1 rates=gamma; prset applyto=(2) statefreqpr=fixed(equal); unlink statefreq=(all) tratio=(all) pinvar=(all) shape=(all); prset applyto=(all) ratepr=variable; mcmcp relburnin=yes burninfrac=0.25 ngen=1000000 nruns=2 nchains=4 printfreq=1000 samplefreq=50 savebrlens=yes; mcmc; sump; sumt contype=allcompat; log stop; END;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ML analysis of Skeletocutis nivea species complex, tef1 dataset --

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

BI analysis of Skeletocutis nivea species complex, tef1 dataset --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN MrBayes; log start filename=niveaTEF1log_CIPRES.txt; set autoclose=yes; CharSet pos1 = 1-139\3 210-345\3 406-721\3 786-879\3; CharSet pos2 = 2-140\3 211-346\3 407-722\3 787-880\3; CharSet pos3 = 3-141\3 212-344\3 405-720\3 785-881\3; CharSet intr = 142-209 347-404 723-784; partition parts = 4: pos1, pos2, pos3, intr; set partition = parts; lset applyto=(1) nst=1 rates=gamma; lset applyto=(2) nst=1 rates=gamma; prset applyto=(2) statefreqpr=fixed(equal); lset applyto=(3) nst=2 rates=gamma; lset applyto=(4) nst=2 rates=propinv; unlink statefreq=(all) tratio=(all) pinvar=(all) shape=(all); prset applyto=(all) ratepr=variable; mcmcp relburnin=yes burninfrac=0.25 ngen=1000000 nruns=2 nchains=4 printfreq=1000 samplefreq=50 savebrlens=yes; mcmc; sump; sumt contype=allcompat; log stop; END;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ML analysis of Skeletocutis nivea species complex, ITS dataset --

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

BI analysis of Skeletocutis nivea species complex, ITS dataset --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN MrBayes; log start filename=nivea_ITS_CIPRES_Bayes.txt; set autoclose=yes; CharSet ITS1et2 = 1-257 412-673; CharSet 5_8S = 258-411; partition parts = 2: ITS1et2, 5_8S; set partition = parts; lset applyto=(1) nst=2 rates=gamma; lset applyto=(2) nst=2; prset applyto=(2) statefreqpr=fixed(equal); unlink statefreq=(all) tratio=(all) pinvar=(all) shape=(all); prset applyto=(all) ratepr=variable; mcmcp relburnin=yes burninfrac=0.25 ngen=10000000 nruns=2 nchains=4 printfreq=1000 samplefreq=50 savebrlens=yes; mcmc; sump; sumt contype=allcompat; log stop; END;

Output data