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groups
groups
 
 
output
output
 
 
parameters
parameters
 
 
trees
trees
 
 
README.md
README.md
 
 
SupFigs1-3-FigTree.tre
SupFigs1-3-FigTree.tre
 
 

README.md

  • The file SupFigs1-3-FigTree.tre is a (FigTree compatible) nexus file including the main ASTRAL tree (Figure S1), the main concatenation tree (Figure S2) and the main Plastid tree (Figure S3). Note the tree is not rooted and has to be rooted manually.

  • The groups folder includes pdf figures (and newick trees) for individual groups within the larger group

  • In addition, we provide all the alternative species trees tested in the onekp paper and shown in Figure S10.

    • The directory trees includes the newick species trees, as detailed below.
    • The directory output includes the results of running DiscoVista with parameters for the DiscoVista are given in the parameters folder.
Directory name Tree name
Full AA
astral_trees_33_percent-FAA ASTRAL-33%-FAA
astral.20.503-FAA ASTRAL-20%-FAA
astral.10.503-FAA ASTRAL-10%-FAA
astral.05.503-FAA ASTRAL-05%-FAA
astral-trees-unbinned-mlbs-raxmlboot.FAA-upp-masked.fasta.mask10sites.mask33taxa.mainlocalpp.tree-FAA ASTRAL-full-FAA
astral-trees-supergenes-mlbs-raxmlboot.FAA-supergene.mainlocalpp.tree-FAA ASTRAL-binning-FAA
upp_masked.fasta.mask10sites.mask33taxa_FAA_alltaxa-FAA CAML-FAA
Full-DNA
astral-trees-unbinned-mlbs-raxmlboot.FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.mainlocalpp.tree-FAA ASTRAL-full-C12
astral-trees-supergenes-mlbs-raxmlboot.FNA2AA-supergene.mainlocalpp.tree-FAA ASTRAL-binning-C12
upp_masked_c12.fasta.mask10sites.mask33taxa_FNA2AA_alltaxa-FAA CAML-C12
plastid_renamed_withsupport.noUAUU.rerooted-FAA Plastid
Filtered-rogue
astral-trees-remove-rogoue-mlbs-raxmlboot.FAA-upp-masked.fasta.mask10sites.mask33taxa.fasttreelocalpp.tree-FAA ASTRAL-remove-rogue-FAA
upp_masked.fasta.mask10sites.mask33taxa_FAA_filtered_remove_rogoue-FAA CAML-remove-rogue-FAA
astral-trees-remove-rogoue-mlbs-raxmlboot.FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.fasttreelocalpp.tree-FAA ASTRAL-remove-rogue-C12
upp_masked_c12.fasta.mask10sites.mask33taxa_FNA2AA_filtered_remove_rogoue-FAA CAML-remove-rogue-C12
Eudicots-only
astral.trees.eudicots.mlbs.raxmlboot.FAA.upp.masked.fasta-mask10sites.mask33taxa.mainlocalpp.tree-FAA ASTRAL-Eudicots-only-FAA
upp_masked.fasta.mask10sites.mask33taxa_FAA_eudicot-FAA CAML-Eudicots-only-FAA
astral-trees-eudicots-mlbs-raxmlboot.FNA2AA-upp-masked-c12.fasta-mask10sites.mask33taxa.mainlocalpp.tree-FAA ASTRAL-Eudicots-only-C12
upp_masked_c12.fasta.mask10sites.mask33taxa_FNA2AA_eudicot-FAA CAML-Eudicots-only-C12