TreeBASE Search-Analyses for study 14268

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Analyses for Study 14268

Citation title: "Latitude drives diversification in Madagascar?s endemic dry forest rodent, Eliurus myoxinus (sub-family Nesomyinae)".

Study name: "Latitude drives diversification in Madagascar?s endemic dry forest rodent, Eliurus myoxinus (sub-family Nesomyinae)".

This study is part of submission 14268 (Status: Published).

Analyses

Analysis 1

Analysis details

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Input data

1 Input object(s)

Analysis step

MrBayes analysis --

Step details

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Software used

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URL
Algorithm
Commands
begin mrbayes; charset pos1 = 1-1089\3; charset pos2 = 2-1089\3; charset pos3 = 3-1089\3; partition allgenes=3: pos1, pos2, pos3; set partition=allgenes; lset applyto=(2) nst=2; lset applyto=(1,3) nst=6; lset applyto=(2) rates=equal; lset applyto=(1,3) rates=gamma; prset applyto=(1) statefreqpr=fixed(equal) ratepr=variable; prset applyto=(2,3) statefreqpr=dirichlet(1,1,1,1) ratepr=variable; [the unlink command unlinks the parameters so they are not shared across partitions] unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all); mcmcp ngen=100000000 printfreq=1000 samplefreq=1000 nchains=1 nrun=2; mcmc; sumt Burninfrac=0.25; quit; end;

Output data

1 Output object(s)

Analysis 2

Analysis details

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Input data

1 Input object(s)

Analysis step

ML Bootstrap analysis --

Step details

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Software used

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Version
URL
Description
Algorithm
Commands
[general] datafname = cytb_garli_boot.nex constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = cytb_garli_boot1.cytb_byCodon 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 resampleproportion = 1.0 inferinternalstateprobs = 0 outputsitelikelihoods = 0 optimizeinputonly = 0 collapsebranches = 1 searchreps = 5 bootstrapreps = 1 linkmodels = 0 subsetspecificrates = 1 [model1] datatype = nucleotide ratematrix = (0 1 0 0 2 0) statefrequencies = equal ratehetmodel = gamma numratecats = 4 invariantsites = none [model2] datatype = nucleotide ratematrix = 2rate statefrequencies = estimate ratehetmodel = none numratecats = 1 invariantsites = none [model3] datatype = nucleotide ratematrix = (0 1 0 0 2 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [master] nindivs = 68 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

Output data

1 Output object(s)