BiopsyTrees             Example Ig lineage trees with biopsy
                        reconstructions.
ExampleAirr             Example AIRR database
ExampleAirrTyCHE        Example AIRR database for TyCHE
ExampleClones           Example Ig lineage trees
ExampleDbChangeo        Example Change-O database
ExampleMixedClones      Example Multiple Partition Trees
ExampleMixedDb          Example Change-O database
IsotypeTrees            Example Ig lineage trees with isotype
                        reconstructions.
TimeTrees               Example Ig lineage trees sampled over time.
airrClone-class         S4 class defining a clone in Dowser
bootstrapTrees          Deprecated! Please use findSwitches instead.
buildAllClonalGermlines
                        buildAllClonalGermlines Determines and builds
                        all possible germlines for a clone
buildBeast              Read in a directory from a BEAST run. Runs
                        treeannotator and loganalyser.
buildClonalGermline     'buildClonalGermline' Determine consensus clone
                        sequence and create germline for clone
buildGermline           'buildGermline' reconstruct germline segments
                        from alignment data
buildIgphyml            Wrapper to build IgPhyML trees and infer
                        intermediate nodes
buildPML                Wrapper for phangorn::optim.pml
buildPhylo              Wrapper for alakazam::buildPhylipLineage
buildPratchet           Wrapper for phangorn::pratchet
buildRAxML              Wrapper to build RAxML-ng trees and infer
                        intermediate nodes
calcRF                  Finds the Robinson-Fould's cluster distance
                        between phylogenies.
checkDivergence         Compare divergence along a tree in terms of
                        mutations (sum of branches) for each tip and
                        reconstructed internal node to its Hamming
                        distance from the germline. Divergence should
                        never be less than Hamming distance.  A
                        threshold of -1 is used to represent 1 full
                        mutation difference. The function will throw a
                        warning if any trees cross this threshold
checkNodeDivergences    For each node in nodes list, check that the
                        current divergence is the same as previously
                        reported
collapseNodes           Collapse internal nodes with the same predicted
                        sequence
colorTrees              Get a color palette for a predefined set of
                        trait values
condenseTrees           Condense a set of equally parsimonious node
                        labels into a single tree
correlationTest         Run date randomization test for temporal signal
                        on a set of trees.
createAllGermlines      createAllGermlines Creates all possible
                        germlines for a clone
createGermlines         createGermlines Determine consensus clone
                        sequence and create germline for clone
create_MRCA_prior_germline
                        Takes an airr clone object and returns BEAST2
                        XML for MRCA prior of the germline sequence
create_MRCA_prior_observed
                        Takes an airr clone object and returns BEAST2
                        XML for MRCA prior of the observed sequences
create_alignment        Takes an airr clone object and returns BEAST2
                        Alignment xml of the sequences
create_height_prior     Takes an airr clone object and returns BEAST2
                        XML to set a height prior
create_max_height_prior
                        Takes an airr clone object and returns BEAST2
                        XML to set a maximum height prior
create_root_freqs       Takes an airr clone object and returns BEAST2
                        rootfreqs xml of the germline
create_starting_tree    Takes an airr clone object and tree and returns
                        BEAST2 XML for setting the starting tree
create_traitset         Takes an airr clone object and returns BEAST2
                        XML for a trait/traitSet from a column
dfToFasta               Write a fasta file of sequences 'readFasta'
                        reads a fasta file
downsampleClone         'downsampleClone' Down-sample clone to maximum
                        tip/switch ratio
dowser                  The dowser package
dowserObjectEquivalent
                        'dowserObjectEquivalent' Experimental. Check if
                        two Dowser objects are equivalent
exportTrees             Exports the phylogenetic trees from the
                        airrClone object
filterCombs             'filterCombs' Remove sequences likely resulting
                        from oversequencing and PCR error This removes
                        "comb" structures in trees which are flat
                        polytomies with low duplicate counts radiating
                        out from a single node with a much higher
                        duplicate count. Adapted from
                        https://bitbucket.org/kleinstein/projects/src/master/Hoehn2022/isotype_analysis/treesAndSwitches_dowser.R
filterPartialSeqs       'filterPartialSeqs'
findSwitches            Create a bootstrap distribution for clone
                        sequence alignments, and estimate trees for
                        each bootstrap replicate.
formatClones            Generate an ordered list of airrClone objects
                        for lineage construction
getAllSeqs              Return all tip and internal node sequences
getBootstraps           Creates a bootstrap distribution for clone
                        sequence alignments, and returns estimated
                        trees for each bootstrap replicate as a nested
                        list as a new input tibble column.
getDiffPoint            Recurse up to tree to find most recent node
                        with different state, or the root
getDiffPoints           For each tree, recurse up to tree to find most
                        recent node with a different state, or the root
getDivergence           Get divergence from root of tree for each tip
getGermline             getGermline get germline segment from specified
                        receptor and segment
getHeightsAndLengths    Add height and length columns to a tree@data
                        data frame
getNodeSeq              Return IMGT gapped sequence of specified tree
                        node
getPalette              Get a color palette for a predefined set of
                        trait values.  'Germline' defaults to black
                        unless specified.
getSeq                  Deprecated! Use getNodeSeq
getSeqPath              Return all sequences along the tree from the
                        germline to a specified node
getSkylines             Make data frames for Bayesian skyline plots
getSubTaxa              Get the tip labels as part of a clade defined
                        by an internal node
getSubclones            #' Deprecated! Use resolveLightChains
getTimeTrees            Estimate time trees by running BEAST on each
                        clone Applies XML 'template' to each clone
getTimeTreesIterate     Iteratively resume getTimeTrees until
                        convergence, as defined by all parameters
                        (except those in 'ignore' vector) having ESS
                        greater than or equal to the specified
                        ess_cutoff
getTrees                Estimate lineage tree topologies, branch
                        lengths, and internal node states if desired
getTreesAndUCAs         getTreesAndUCAs Construct trees and infer the
                        UCA
installPythonDependencies
                        installPythonDependencies Checks for and
                        installs the Python dependencies for UCA
                        estimation
makeAirrClone           Generate a airrClone object for lineage
                        construction
makeModelFile           Make a parsimony model file
makeSkyline             get values for Bayesian Skyline plot
mapSubtrees             Get a map of nodes from one
maskCodons              'maskCodons' Masks codons split by insertions
maskSequences           'maskSequences' Mask codons split by insertions
                        in V gene
plotMSA                 Simple function for plotting multiple sequence
                        alignments input can be either nucleotide or AA
                        and contain ambiguous characters
plotSkylines            Simple function for plotting Bayesian skyline
                        plots
plotTrees               Plot a tree with colored internal node labels
                        using ggtree
readBEAST               Reads in a BEAST output directory
readFasta               Read a fasta file into a list of sequences
                        'readFasta' reads a fasta file
readIMGT                'readIMGT' read in IMGT database
readLineages            Read in all trees from a lineages file
readModelFile           Read in a parsimony model file
readTreesJSON           'readTreesJSON' Experimental. Read trees from
                        JSON/AIRR format from Dowser
reconIgPhyML            Do IgPhyML maximum parsimony reconstruction
rerootTree              Reroot phylogenetic tree to have its germline
                        sequence at a zero-length branch to a node
                        which is the direct ancestor of the tree's UCA.
                        Assigns 'uca' to be the ancestral node to the
                        tree's germline sequence, as 'germid' as the
                        tree's germline sequence ID.
resolveLightChains      Define subgroups within clones based on light
                        chain rearrangements
resolvePolytomies       Resolve polytomies to have the minimum number
                        of single timepoint clades
runCorrelationTest      Run correlationTest, based on
                        https://doi.org/10.1111/2041-210X.12466
sampleCloneMultiGroup   'sampleCloneMultiGroup' Down-sample clone to
                        specified size with one or multiple groups to
                        sample evenly
sampleClones            'sampleClones' Down-sample clones to specified
                        size
scaleBranches           Scale branch lengths to represent either
                        mutations or mutations per site.
setNodeDivergences      For each node in nodes list, store the
                        divergence from the UCA
stitchRegions           stitchRegions Similar to stitchVDJ but with
                        segment IDs instead of nucleotides
stitchVDJ               stitchVDJ combines germline gene segments to a
                        single string
stopCodonCheck          Check whether sequences have in-frame premature
                        stop codons (PTCs)
testPS                  Performs PS (parsimony score) test on switch
                        data
testSC                  Performs SC (switch count) test on switch data
testSP                  Performs SP (switch proportion) test on switch
                        data
treesEquivalent         Check whether two tree objects are equivalent
treesToPDF              Simple function for plotting a lot of trees
                        into a pdf
writeCloneSequences     Write the sequences used in tree building to a
                        fasta format. If there are more than one tree
                        in airrClone output the sequence id will be
                        followed by "|clone_id".
writeFasta              'writeFasta' Write a fasta file of sequences
                        given a named list of sequences
writeLineageFile        Write lineage file for IgPhyML use
writeTreesJSON          'writeTreesJSON' Experimental. Write trees in
                        AIRR format
write_clone_to_xml      Takes an airr clone object and template and
                        writes a BEAST2 XML file
write_clones_to_xmls    Wrapper to write multiple clones to XML files
