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Analyses for Study 18487

Citation title: "Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology".

Study name: "Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology".

This study is part of submission 18487 (Status: Published).

Analyses

Analysis 1

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Software used

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Commands
begin mrbayes; log start file=CO1_150211_2.nex.log; set autoclose=yes nowarn=yes; outgroup 1; charset 1st+2nd = 2-658\3 3-658\3; charset 3rd = 1-658\3; partition codon_positions=2: 1st+2nd, 3rd; set partition=codon_positions; Lset applyto=(all) nst=6 rates=invgamma; unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all); prset applyto=(all) statefreqpr=dirichlet(1,1,1,1) ratepr=variable; mcmcp ngen=10000000 nruns=2 nchains=8 samplefreq=100 printfreq=100 relburnin=yes burninfrac=0.25 savebrlens=yes printmax=16; mcmc; sumt relburnin=yes burninfrac=0.25; sump relburnin=yes burninfrac=0.25; end;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Output data

1 Output object(s)

Analysis 3

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Notes

Software used

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Version
URL
Algorithm
Commands
{DATAFILE} Data file = d:\Analyses15-04-24PHASE_28S\LSU_15-04-24AP.phase Interleaved data file = no Heterogeneous data models = auto {\DATAFILE} {MODEL} Model = MIXED Number of models = 2 {MODEL1} Model = REV Discrete gamma distribution of rates = yes Number of gamma categories = 4 Invariant sites = no {\MODEL1} {MODEL2} Model = RNA16C Discrete gamma distribution of rates = yes Number of gamma categories = 4 Invariant sites = no {\MODEL2} {\MODEL} {TREE} Tree = Unrooted MCMC tree Outgroup=Suberites_ficus_BELUM_MC4322 {\TREE} {PERTURBATION} Tree, proposal priority = 2 Model, proposal priority = 10 {PERTURBATION_TREE} Topology changes, proposal priority = 10 Branch lengths, proposal priority = 40 Hyperpriors, proposal priority = 2 Branch lengths, prior = exponential(uniform(0,100)) Branch lengths exponential hyperparameter, proposal priority = 1 {\PERTURBATION_TREE} {PERTURBATION_MODEL} Model 1, proposal priority = 11 Model 2, proposal priority = 21 Average rates, proposal priority = 1 {PERTURBATION_MODEL1} Frequencies, proposal priority = 2 Rate ratios, proposal priority = 1 Gamma parameter, proposal priority = 1 {\PERTURBATION_MODEL1} {PERTURBATION_MODEL2} Frequencies, proposal priority = 2 Rate ratios, proposal priority = 10 Gamma parameter, proposal priority = 1 {\PERTURBATION_MODEL2} {\PERTURBATION_MODEL} {\PERTURBATION} Random seed = 1234 Burnin iterations = 1000000 Sampling iterations = 15000000 Sampling period = 200 Output file = d:\Analyses15-04-24PHASE_28S\LSU_15-04-24AP1R1 Output format = phylip

Output data

2 Output object(s)

Analysis 4

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Notes

Software used

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Version
URL
Algorithm
Commands
{DATAFILE} Data file = input-data/regions_AP_4phase.phase Interleaved data file = no Heterogeneous data models = auto {\DATAFILE} {MODEL} Model = MIXED Number of models = 2 {MODEL1} Model = REV Discrete gamma distribution of rates = yes Number of gamma categories = 4 Invariant sites = no {\MODEL1} {MODEL2} Model = RNA16C Discrete gamma distribution of rates = yes Number of gamma categories = 4 Invariant sites = no {\MODEL2} {\MODEL} {TREE} Tree = Unrooted MCMC tree Outgroup=Suberites_ficus_BELUM_MC4322 {\TREE} {PERTURBATION} Tree, proposal priority = 2 Model, proposal priority = 10 {PERTURBATION_TREE} Topology changes, proposal priority = 10 Branch lengths, proposal priority = 40 Hyperpriors, proposal priority = 2 Branch lengths, prior = exponential(uniform(0,100)) Branch lengths exponential hyperparameter, proposal priority = 1 {\PERTURBATION_TREE} {PERTURBATION_MODEL} Model 1, proposal priority = 11 Model 2, proposal priority = 21 Average rates, proposal priority = 1 {PERTURBATION_MODEL1} Frequencies, proposal priority = 2 Rate ratios, proposal priority = 1 Gamma parameter, proposal priority = 1 {\PERTURBATION_MODEL1} {PERTURBATION_MODEL2} Frequencies, proposal priority = 2 Rate ratios, proposal priority = 10 Gamma parameter, proposal priority = 1 {\PERTURBATION_MODEL2} {\PERTURBATION_MODEL} {\PERTURBATION} Random seed = 1234 Burnin iterations = 1000000 Sampling iterations = 30000000 Sampling period = 200 Output file = regions_AP_4phase_run2 Output format = phylip

Output data

2 Output object(s)

Analysis 5

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Notes

Software used

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Version
URL
Algorithm
Commands
{DATAFILE} Data file=LSU_CO1_15-10-15AP.phase Interleaved data file=no Interleaved structure=no Heterogeneous data models=yes {\DATAFILE} {MODEL} Model=MIXED Number of models=4 {MODEL1} Model=RNA16C Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=no {\MODEL1} {MODEL2} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=no {\MODEL2} {MODEL3} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=yes {\MODEL3} {MODEL4} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=yes {\MODEL4} {\MODEL} {TREE} Tree=Unrooted MCMC tree Outgroup=Suberites_ficus_BELUM_MC4322 {\TREE}

Output data

2 Output object(s)

Analysis 6

Analysis details

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Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Notes

Software used

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Commands
{DATAFILE} Data file=D:\X\LSU_CO1_15-10-15AP_reduced.phase Interleaved data file=no Interleaved structure=no Heterogeneous data models=yes {\DATAFILE} {MODEL} Model=MIXED Number of models=4 {MODEL1} Model=RNA16C Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=no {\MODEL1} {MODEL2} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=no {\MODEL2} {MODEL3} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=yes {\MODEL3} {MODEL4} Model=REV Discrete gamma distribution of rates=yes Number of gamma categories=4 Invariant sites=yes {\MODEL4} {\MODEL} {TREE} Tree=Unrooted MCMC tree Outgroup=Suberites_ficus_BELUM_MC4322 {\TREE}

Output data

2 Output object(s)

Analysis 7

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ML analysis --

Output data