TreeBASE Search-Analyses for study 17840

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Analyses for Study 17840

Citation title: "Phylogeny of Sparganium (Typhaceae) revisited: Non-monophyletic nature of S. emersum sensu lato and resurrection of S. acaule".

Study name: "Phylogeny of Sparganium (Typhaceae) revisited: Non-monophyletic nature of S. emersum sensu lato and resurrection of S. acaule".

This study is part of submission 17840 (Status: Published).

Analyses

Analysis 1

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_ptDNA_MP --

Step details

Name
Notes

Software used

Name
Algorithm
Commands
Sparganium_erectum 0111011100001 Sparganium_hyperboreum 0101010000001 Sparganium_natans 0101010000001 Sparganium_androcladum 0101011100011 Sparganium_angustifolium_NEB314272 0001011100001 Sparganium_angustifolium_DAO825670 0101011100001 Sparganium_acaule 1101000100001 Sparganium_emersum 0101011100001 Sparganium_fallax 0100011101001 Sparganium_fluitans 0101011100110 Sparganium_glomeratum 1101000110001 Sparganium_gramineum 0101011100110 Sparganium_japonicum 1101111100001 Sparganium_subglobosum 0101011100001 begin paup; set autoclose=yes warnreset=no increase=prompt; set criterion=parsimony; hsearch addseq=random; pset opt=acctran; roottrees outroot=monophyl; showtree; describetrees 1/ plot=phylogram brlens=yes; savetrees file=Sparganium_ptDNA.tre brlens=yes; contree all/strict=yes tcompress=yes treefile=Sparganium_ptDNA_contree.tre; bootstrap nrep=1000 treefile=Sparganium_ptDNA_bs.tre; end;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_phyC_MP --

Step details

Name
Notes

Software used

Name
Algorithm
Commands
begin paup; set autoclose=yes warnreset=no increase=prompt; set criterion=parsimony; hsearch addseq=random; pset opt=acctran; roottrees outroot=monophyl; showtree; describetrees 1/ plot=phylogram brlens=yes; savetrees file=Sparganium_phyC.tre brlens=yes; contree all/strict=yes tcompress=yes treefile=Sparganium_phyC_contree.tre; bootstrap nrep=1000 treefile=Sparganium_phyC_bs.tre; end;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_ptDNA_RAxML --

Output data

1 Output object(s)

Analysis 4

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_phyC_RAxML --

Output data

1 Output object(s)

Analysis 5

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_ptDNA_MrBayes --

Step details

Name
Notes

Software used

Name
Algorithm
Commands
Sparganium_erectum 0111011100001 Sparganium_hyperboreum 0101010000001 Sparganium_natans 0101010000001 Sparganium_androcladum 0101011100011 Sparganium_angustifolium_NEB314272 0001011100001 Sparganium_angustifolium_DAO825670 0101011100001 Sparganium_acaule 1101000100001 Sparganium_emersum 0101011100001 Sparganium_fallax 0100011101001 Sparganium_fluitans 0101011100110 Sparganium_glomeratum 1101000110001 Sparganium_gramineum 0101011100110 Sparganium_japonicum 1101111100001 Sparganium_subglobosum 0101011100001 begin mrbayes; charset morphology = 1-13; charset molecules = 14-5987; partition favored = 2: morphology, molecules; set partition = favored; Lset applyto=(1) nst=1 rates=equal; Prset ratepr=variable; end;

Output data

2 Output object(s)

Analysis 6

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Sparganium_phyC_MrBayes --

Output data