TreeBASE Search-Analyses for study 17344

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Analyses for Study 17344

Citation title: "Highly polytypic taxon complex: integrative taxonomic assessment of the widespread polytypic pollinator Bombus pascuorum (Hymenoptera: Apidae)".

Study name: "Highly polytypic taxon complex: integrative taxonomic assessment of the widespread polytypic pollinator Bombus pascuorum (Hymenoptera: Apidae)".

This study is part of submission 17344 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
[BEAST input file generated via BEAUTiAutomator (available at https://github.com/michaelgruenstaeudl/BEAUTiAutomator)]

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
[BEAST input file generated via BEAUTiAutomator (available at https://github.com/michaelgruenstaeudl/BEAUTiAutomator)]

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
[BEAST input file generated via BEAUTiAutomator (available at https://github.com/michaelgruenstaeudl/BEAUTiAutomator)]

Output data

1 Output object(s)

Analysis 4

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Likelihood estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Commands
[general] datafname = A19.input constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = A19.output randseed = -1 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 searchreps = 100 [model1] [set to HKY+G] datatype = nucleotide ratematrix = 2rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0 bootstrapreps = 0 resampleproportion = 1.0 inferinternalstateprobs = 0

Output data

1 Output object(s)

Analysis 5

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Likelihood estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Commands
[general] datafname = B12.input constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = B12.output randseed = -1 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 searchreps = 100 [model1] [set to TrN+I] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = none numratecats = 4 invariantsites = estimate [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0 bootstrapreps = 0 resampleproportion = 1.0 inferinternalstateprobs = 0

Output data

1 Output object(s)

Analysis 6

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Likelihood estimation of gene trees --

Step details

Name

Software used

Name
Version
URL
Commands
[general] datafname = ETS.input constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = ETS.output randseed = -1 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 searchreps = 100 [model1] [set to GTR+G] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0 bootstrapreps = 0 resampleproportion = 1.0 inferinternalstateprobs = 0

Output data