TreeBASE Search-Analyses for study 25164

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Analyses for Study 25164

Citation title: "Bleximothyrites ostiolatus gen. et sp. nov. a unique fly-speck fungus (Dothideomycetes) from the Lower Cretaceous Potomac Group, lower Zone 1, of Virginia ".

Study name: "Bleximothyrites ostiolatus gen. et sp. nov. a unique fly-speck fungus (Dothideomycetes) from the Lower Cretaceous Potomac Group, lower Zone 1, of Virginia ".

This study is part of submission 25164 (Status: Published).

Analyses

Analysis 1

Analysis details

Name
Notes

Input data

5 Input object(s)

Analysis step

MLTree --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
raxmlHPC-HYBRID -T 4 -s infile.phy -E excludefile.txt -m GTRGAMMA -p 12345 -q part -k -f d -N 500 0 -n infile.tre raxmlHPC-PTHREADS -T 12 -f b -n 1KMLbest -s infile.phy -E excludefile.txt -m GTRGAMMA -p 12345 -t tree.tre -q part.txt -z topologies_file.tre excludefile.txt 41-41 94-94 115-115 149-149 269-269 299-299 377-381 536-536 581-606 634-666 677-678 757-759 808-808 990-1013 1026-1026 1039-1046 1070-1077 1185-1185 1197-1197 1317-1326 1349-1361 1577-1694 1725-1746 1779-1797 1814-1832 1860-1885 2074-2082 2099-2141 2158-2158 2177-2180 2199-2222 2237-2237 2251-2264 2344-2362 2380-2381 2397-2413 2430-2446 2476-2476 2540-2540 2625-2625 2655-2656 2707-2707 2746-2746 3022-3040 3101-4697

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

5 Input object(s)

Analysis step

MrBayes Tree --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
begin mrbayes; log start filename=infile.nex; MrBayes > exclude 41-41 MrBayes > exclude 94-94 MrBayes > exclude 115-115 MrBayes > exclude 149-149 MrBayes > exclude 269-269 MrBayes > exclude 299-299 MrBayes > exclude 377-381 MrBayes > exclude 536-536 MrBayes > exclude 581-606 MrBayes > exclude 634-666 MrBayes > exclude 677-678 MrBayes > exclude 757-759 MrBayes > exclude 808-808 MrBayes > exclude 990-1013 MrBayes > exclude 1026-1026 MrBayes > exclude 1039-1046 MrBayes > exclude 1070-1077 MrBayes > exclude 1185-1185 MrBayes > exclude 1197-1197 MrBayes > exclude 1317-1326 MrBayes > exclude 1349-1361 MrBayes > exclude 1577-1694 MrBayes > exclude 1725-1746 MrBayes > exclude 1779-1797 MrBayes > exclude 1814-1832 MrBayes > exclude 1860-1885 MrBayes > exclude 2074-2082 MrBayes > exclude 2099-2141 MrBayes > exclude 2158-2158 MrBayes > exclude 2177-2180 MrBayes > exclude 2199-2222 MrBayes > exclude 2237-2237 MrBayes > exclude 2251-2264 MrBayes > exclude 2344-2362 MrBayes > exclude 2380-2381 MrBayes > exclude 2397-2413 MrBayes > exclude 2430-2446 MrBayes > exclude 2476-2476 MrBayes > exclude 2540-2540 MrBayes > exclude 2625-2625 MrBayes > exclude 2655-2656 MrBayes > exclude 2707-2707 MrBayes > exclude 2746-2746 MrBayes > exclude 3022-3040 MrBayes > exclude 3101-4697 partition genes = 2: 1-1435, 1436-2578; set partition = genes; lset applyto=(all) rates=invgamma nst=mixed; unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all) [brlens = (all)] ; prset applyto=(all) ratepr=variable; set autoclose=yes; report possel=yes; showmodel; mcmc ngen=20000000 printfreq=1000 nruns=2 samplefreq=1000 nchains=4 savebrlens=yes filename=output.out; sump burninfrac=0.25 filename=output.out; sumt burninfrac=0.25 filename=output.out; log stop;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Fossil_MaxParsimony_ML --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
Branch-and-bound search settings: Optimality criterion = parsimony Character-status summary: Of 9 total characters: All characters are of type 'unord' All characters have equal weight 1 character is parsimony-uninformative Number of parsimony-informative characters = 8 Gaps are treated as "missing" Initial upper bound: unknown (compute heuristically) Addition sequence: furthest Initial 'Maxtrees' setting = 100 Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Keeping only trees compatible with constraint-tree "Imported tree 1" Trees are unrooted

Output data

1 Output object(s)

Analysis 4

Analysis details

Input data

5 Input object(s)

Analysis step

PP on MLtree --

Output data