Files in BobLiterman/Rboretum
Compare Phylogenetic Trees and Alignment Support Values

.gitignore

DESCRIPTION

NAMESPACE

R/checkTips.R R/checkValidFiles.R R/combineBootstraps.R R/convertLabels.R R/detectSingleRoot.R R/extractNodeAges.R R/getAlignmentBreakdown.R R/getAlignmentComposition.R R/getAlignmentPatterns.R R/getAlignmentSignal.R R/getAlignmentSpecies.R R/getAlignmentSupport.R R/getSharedTaxa.R R/getSpeciesComposition.R R/getTreeClades.R R/getTreeRoot.R R/getTreeSplits.R R/getTreeSplits_Worker.R R/getUniqueTopologies.R R/isAlignmentSignal.R R/isAlignmentSupport.R R/isCladeSupport.R R/isMultiPhylo.R R/isPhylo.R R/isPlot.R R/pie_inset.R R/readRooted.R R/readRooted_Worker.R R/rescaleTreeSupport.R R/semiChecker.R R/semiSorter.R R/semiVector.R R/sourceRboretum.R R/stripNodeLabels.R R/summarizeMultiPhylo.R R/tableCount.R R/tandemPlotter.R R/timePlotter.R R/time_lm.R R/treeDater.R R/treeNamer.R R/treePlotter.R R/treeTrimmer.R R/vectorSemi.R README.md

docs/Makefile

docs/build/doctrees/content/alignment_functions/getAlignmentBreakdown.doctree

docs/build/doctrees/content/alignment_functions/getAlignmentComposition.doctree

docs/build/doctrees/content/alignment_functions/getAlignmentPatterns.doctree

docs/build/doctrees/content/alignment_functions/getAlignmentSignal.doctree

docs/build/doctrees/content/alignment_functions/getAlignmentSpecies.doctree

docs/build/doctrees/content/alignment_functions/getAlignmentSupport.doctree

docs/build/doctrees/content/alignment_functions/getSpeciesComposition.doctree

docs/build/doctrees/content/installation.doctree

docs/build/doctrees/content/loading.doctree

docs/build/doctrees/content/plotting_functions/tandemPlotter.doctree

docs/build/doctrees/content/plotting_functions/timePlotter.doctree

docs/build/doctrees/content/plotting_functions/treePlotter.doctree

docs/build/doctrees/content/rboretum-suite.doctree

docs/build/doctrees/content/tree_functions/checkTips.doctree

docs/build/doctrees/content/tree_functions/extractNodeAges.doctree

docs/build/doctrees/content/tree_functions/getSharedTaxa.doctree

docs/build/doctrees/content/tree_functions/getTreeClades.doctree

docs/build/doctrees/content/tree_functions/getTreeRoot.doctree

docs/build/doctrees/content/tree_functions/getTreeSplits.doctree

docs/build/doctrees/content/tree_functions/getUniqueTopologies.doctree

docs/build/doctrees/content/tree_functions/readRooted.doctree

docs/build/doctrees/content/tree_functions/summarizeMultiphylo.doctree

docs/build/doctrees/content/tree_functions/treeDater.doctree

docs/build/doctrees/content/tree_functions/treeNamer.doctree

docs/build/doctrees/content/tree_functions/treeTrimmer.doctree

docs/build/doctrees/content/utility_functions/convertLabels.doctree

docs/build/doctrees/content/utility_functions/semiSorter.doctree

docs/build/doctrees/content/utility_functions/semiVector.doctree

docs/build/doctrees/content/utility_functions/tableCount.doctree

docs/build/doctrees/content/utility_functions/vectorSemi.doctree

docs/build/doctrees/environment.pickle

docs/build/doctrees/index.doctree

docs/build/html/.buildinfo

docs/build/html/_images/Dummy_Align.png

docs/build/html/_images/checkTips.png

docs/build/html/_images/tandemPlotter_1.png

docs/build/html/_images/tandemPlotter_2.png

docs/build/html/_images/tandemPlotter_3.png

docs/build/html/_images/timePlotter.png

docs/build/html/_images/treePlotter_1.png

docs/build/html/_images/treePlotter_10.png

docs/build/html/_images/treePlotter_11.png

docs/build/html/_images/treePlotter_12.png

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docs/build/html/_images/treePlotter_6.png

docs/build/html/_images/treePlotter_7.png

docs/build/html/_images/treePlotter_8.png

docs/build/html/_images/treePlotter_9.png

docs/build/html/_sources/content/alignment_functions/getAlignmentBreakdown.rst.txt

docs/build/html/_sources/content/alignment_functions/getAlignmentComposition.rst.txt

docs/build/html/_sources/content/alignment_functions/getAlignmentPatterns.rst.txt

docs/build/html/_sources/content/alignment_functions/getAlignmentSignal.rst.txt

docs/build/html/_sources/content/alignment_functions/getAlignmentSpecies.rst.txt

docs/build/html/_sources/content/alignment_functions/getAlignmentSupport.rst.txt

docs/build/html/_sources/content/alignment_functions/getSpeciesComposition.rst.txt

docs/build/html/_sources/content/installation.rst.txt

docs/build/html/_sources/content/loading.rst.txt

docs/build/html/_sources/content/plotting_functions/tandemPlotter.rst.txt

docs/build/html/_sources/content/plotting_functions/timePlotter.rst.txt

docs/build/html/_sources/content/plotting_functions/treePlotter.rst.txt

docs/build/html/_sources/content/rboretum-suite.rst.txt

docs/build/html/_sources/content/tree_functions/checkTips.rst.txt

docs/build/html/_sources/content/tree_functions/extractNodeAges.rst.txt

docs/build/html/_sources/content/tree_functions/getSharedTaxa.rst.txt

docs/build/html/_sources/content/tree_functions/getTreeClades.rst.txt

docs/build/html/_sources/content/tree_functions/getTreeRoot.rst.txt

docs/build/html/_sources/content/tree_functions/getTreeSplits.rst.txt

docs/build/html/_sources/content/tree_functions/getUniqueTopologies.rst.txt

docs/build/html/_sources/content/tree_functions/readRooted.rst.txt

docs/build/html/_sources/content/tree_functions/summarizeMultiphylo.rst.txt

docs/build/html/_sources/content/tree_functions/treeDater.rst.txt

docs/build/html/_sources/content/tree_functions/treeNamer.rst.txt

docs/build/html/_sources/content/tree_functions/treeTrimmer.rst.txt

docs/build/html/_sources/content/utility_functions/convertLabels.rst.txt

docs/build/html/_sources/content/utility_functions/semiSorter.rst.txt

docs/build/html/_sources/content/utility_functions/semiVector.rst.txt

docs/build/html/_sources/content/utility_functions/tableCount.rst.txt

docs/build/html/_sources/content/utility_functions/vectorSemi.rst.txt

docs/build/html/_sources/index.rst.txt

docs/build/html/_static/RAL_Style.css

docs/build/html/_static/Rboretum_Logo.png

docs/build/html/_static/basic.css

docs/build/html/_static/css/badge_only.css

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docs/build/html/content/alignment_functions/getAlignmentSignal.html

docs/build/html/content/alignment_functions/getAlignmentSpecies.html

docs/build/html/content/alignment_functions/getAlignmentSupport.html

docs/build/html/content/alignment_functions/getSpeciesComposition.html

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docs/build/html/content/loading.html

docs/build/html/content/plotting_functions/tandemPlotter.html

docs/build/html/content/plotting_functions/timePlotter.html

docs/build/html/content/plotting_functions/treePlotter.html

docs/build/html/content/rboretum-suite.html

docs/build/html/content/tree_functions/checkTips.html

docs/build/html/content/tree_functions/extractNodeAges.html

docs/build/html/content/tree_functions/getSharedTaxa.html

docs/build/html/content/tree_functions/getTreeClades.html

docs/build/html/content/tree_functions/getTreeRoot.html

docs/build/html/content/tree_functions/getTreeSplits.html

docs/build/html/content/tree_functions/getUniqueTopologies.html

docs/build/html/content/tree_functions/readRooted.html

docs/build/html/content/tree_functions/summarizeMultiphylo.html

docs/build/html/content/tree_functions/treeDater.html

docs/build/html/content/tree_functions/treeNamer.html

docs/build/html/content/tree_functions/treeTrimmer.html

docs/build/html/content/utility_functions/convertLabels.html

docs/build/html/content/utility_functions/semiSorter.html

docs/build/html/content/utility_functions/semiVector.html

docs/build/html/content/utility_functions/tableCount.html

docs/build/html/content/utility_functions/vectorSemi.html

docs/build/html/genindex.html

docs/build/html/index.html

docs/build/html/objects.inv

docs/build/html/search.html

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docs/desktop.ini

docs/make.bat

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docs/source/_templates/layout.html

docs/source/conf.py

docs/source/content/alignment_functions/getAlignmentBreakdown.rst

docs/source/content/alignment_functions/getAlignmentComposition.rst

docs/source/content/alignment_functions/getAlignmentPatterns.rst

docs/source/content/alignment_functions/getAlignmentSignal.rst

docs/source/content/alignment_functions/getAlignmentSpecies.rst

docs/source/content/alignment_functions/getAlignmentSupport.rst

docs/source/content/alignment_functions/getSpeciesComposition.rst

docs/source/content/images/Dummy_Align.png

docs/source/content/images/Rboretum_Logo.png

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docs/source/content/installation.rst

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docs/source/content/plotting_functions/tandemPlotter.rst

docs/source/content/plotting_functions/timePlotter.rst

docs/source/content/plotting_functions/treePlotter.rst

docs/source/content/rboretum-suite.rst

docs/source/content/tree_functions/checkTips.rst

docs/source/content/tree_functions/extractNodeAges.rst

docs/source/content/tree_functions/getSharedTaxa.rst

docs/source/content/tree_functions/getTreeClades.rst

docs/source/content/tree_functions/getTreeRoot.rst

docs/source/content/tree_functions/getTreeSplits.rst

docs/source/content/tree_functions/getUniqueTopologies.rst

docs/source/content/tree_functions/readRooted.rst

docs/source/content/tree_functions/summarizeMultiphylo.rst

docs/source/content/tree_functions/treeDater.rst

docs/source/content/tree_functions/treeNamer.rst

docs/source/content/tree_functions/treeTrimmer.rst

docs/source/content/utility_functions/convertLabels.rst

docs/source/content/utility_functions/semiSorter.rst

docs/source/content/utility_functions/semiVector.rst

docs/source/content/utility_functions/tableCount.rst

docs/source/content/utility_functions/vectorSemi.rst

docs/source/index.rst

inst/Add_Ns.py

inst/Alignment_Composition.py

inst/Alignment_Patterns.py

inst/Alignment_Species.py

inst/Alignment_Splits.py

inst/Rboretum_pyRun.py

inst/Species_Composition.py

inst/extdata/Data_Simulation/Raw/Add_Ns.py

inst/extdata/Data_Simulation/Raw/Missing_Table.tsv

inst/extdata/Data_Simulation/Raw/Out_10_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_1_Sm_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_1_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_2_Sm_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_2_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_3_Sm_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_3_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_4_Sm_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_4_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_5_Sm_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_5_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_6_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_7_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_8_TRUE.phy

inst/extdata/Data_Simulation/Raw/Out_9_TRUE.phy

inst/extdata/Data_Simulation/Raw/Python_AddN.sh

inst/extdata/Data_Simulation/Raw/generate_Missing.R

inst/extdata/Data_Simulation/generation/LOG.txt

inst/extdata/Data_Simulation/generation/Out_1.fas

inst/extdata/Data_Simulation/generation/Out_10.fas

inst/extdata/Data_Simulation/generation/Out_10_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_1_Sm.fas

inst/extdata/Data_Simulation/generation/Out_1_Sm_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_1_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_2.fas

inst/extdata/Data_Simulation/generation/Out_2_Sm.fas

inst/extdata/Data_Simulation/generation/Out_2_Sm_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_2_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_3.fas

inst/extdata/Data_Simulation/generation/Out_3_Sm.fas

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inst/extdata/Data_Simulation/generation/Out_3_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_4.fas

inst/extdata/Data_Simulation/generation/Out_4_Sm.fas

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inst/extdata/Data_Simulation/generation/Out_4_TRUE.phy

inst/extdata/Data_Simulation/generation/Out_5.fas

inst/extdata/Data_Simulation/generation/Out_5_Sm.fas

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inst/extdata/Data_Simulation/generation/Out_6.fas

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inst/extdata/Data_Simulation/generation/control_Walkthrough.txt

inst/extdata/Data_Simulation/generation/indelible_1.03_Windows.exe

inst/extdata/Data_Simulation/generation/trees.txt

inst/extdata/Data_Simulation/withN/Gene_1.phy

inst/extdata/Data_Simulation/withN/Gene_10.phy

inst/extdata/Data_Simulation/withN/Gene_1_Small.phy

inst/extdata/Data_Simulation/withN/Gene_2.phy

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inst/extdata/Data_Simulation/withN/Gene_3.phy

inst/extdata/Data_Simulation/withN/Gene_3_Small.phy

inst/extdata/Data_Simulation/withN/Gene_4.phy

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inst/extdata/Data_Simulation/withN/Gene_6.phy

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inst/extdata/Data_Simulation/withN/Gene_8.phy

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inst/extdata/Name_Conversion_Table.tsv

inst/extdata/Walkthrough/Alignments/Gene_1.phy

inst/extdata/Walkthrough/Alignments/Gene_10.phy

inst/extdata/Walkthrough/Alignments/Gene_2.phy

inst/extdata/Walkthrough/Alignments/Gene_3.phy

inst/extdata/Walkthrough/Alignments/Gene_4.phy

inst/extdata/Walkthrough/Alignments/Gene_5.phy

inst/extdata/Walkthrough/Alignments/Gene_6.phy

inst/extdata/Walkthrough/Alignments/Gene_7.phy

inst/extdata/Walkthrough/Alignments/Gene_8.phy

inst/extdata/Walkthrough/Alignments/Gene_9.phy

inst/extdata/alignments/Dummy_Alignment.fa

inst/extdata/alignments/Gene_1.phy

inst/extdata/alignments/Gene_2.phy

inst/extdata/alignments/Gene_3.phy

inst/extdata/alignments/Gene_4.phy

inst/extdata/alignments/Gene_5.phy

inst/extdata/timeTrees/Gene_1_TimeTree.nwk

inst/extdata/timeTrees/Gene_2_TimeTree.nwk

inst/extdata/timeTrees/Gene_3_TimeTree.nwk

inst/extdata/timeTrees/Gene_4_TimeTree.nwk

inst/extdata/timeTrees/Gene_5_TimeTree.nwk

inst/extdata/unrootedTrees/Gene_1.nwk

inst/extdata/unrootedTrees/Gene_2.nwk

inst/extdata/unrootedTrees/Gene_3.nwk

inst/extdata/unrootedTrees/Gene_4.nwk

inst/extdata/unrootedTrees/Gene_5.nwk

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.

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BobLiterman/Rboretum
Compare Phylogenetic Trees and Alignment Support Values

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Compare Phylogenetic Trees and Alignment Support Values

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BobLiterman/Rboretum Compare Phylogenetic Trees and Alignment Support Values

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BobLiterman/Rboretum
Compare Phylogenetic Trees and Alignment Support Values

Files in BobLiterman/Rboretum
Compare Phylogenetic Trees and Alignment Support Values