| airrClone-class | S4 class defining a clone in Dowser |
| BiopsyTrees | Example Ig lineage trees with biopsy reconstructions. |
| bootstrapTrees | Deprecated! Please use findSwitches instead. |
| buildClonalGermline | 'buildClonalGermline' Determine consensus clone sequence and... |
| buildGermline | 'buildGermline' reconstruct germline segments from alignment... |
| buildIgphyml | Wrapper to build IgPhyML trees and infer intermediate nodes |
| buildPhylo | Wrapper for alakazam::buildPhylipLineage |
| buildPML | Wrapper for phangorn::optim.pml |
| 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... |
| 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... |
| correlationTest | Run date randomization test for temporal signal on a set of... |
| createGermlines | createGermlines Determine consensus clone sequence and create... |
| downsampleClone | 'downsampleClone' Down-sample clone to maximum tip/switch... |
| dowser | The dowser package |
| dowser-package | dowser: B Cell Receptor Phylogenetics Toolkit |
| ExampleAirr | Example AIRR database |
| ExampleClones | Example Ig lineage trees |
| ExampleDbChangeo | Example Change-O database |
| ExampleMixedClones | Example Multiple Partition Trees |
| ExampleMixedDb | Example Change-O database |
| findSwitches | Create a bootstrap distribution for clone sequence... |
| formatClones | Generate an ordered list of airrClone objects for lineage... |
| getBootstraps | Creates a bootstrap distribution for clone sequence... |
| getDivergence | Get divergence from root of tree for each tip |
| getGermline | getGermline get germline segment from specified receptor and... |
| getNodeSeq | Return IMGT gapped sequence of specified tree node |
| getPalette | Get a color palette for a predefined set of trait values.... |
| getSeq | Deprecated! Use getNodeSeq |
| getSubclones | #' Deprecated! Use resolveLightChains |
| getSubTaxa | Get the tip labels as part of a clade defined by an internal... |
| getTrees | Estimate lineage tree topologies, branch lengths, and... |
| IsotypeTrees | Example Ig lineage trees with isotype reconstructions. |
| makeAirrClone | Generate a airrClone object for lineage construction |
| makeModelFile | Make a parsimony model file |
| maskCodons | 'maskCodons' Masks codons split by insertions |
| maskSequences | 'maskSequences' Mask codons split by insertions in V gene |
| plotTrees | Plot a tree with colored internal node labels using ggtree |
| readFasta | Read a fasta file into a list of sequences 'readFasta' reads... |
| readIMGT | 'readIMGT' read in IMGT database |
| readLineages | Read in all trees from a lineages file |
| readModelFile | Read in a parsimony model file |
| reconIgPhyML | Do IgPhyML maximum parsimony reconstruction |
| rerootTree | Reroot phylogenetic tree to have its germline sequence at a... |
| resolveLightChains | Define subgroups within clones based on light chain... |
| resolvePolytomies | Resolve polytomies to have the minimum number of single... |
| runCorrelationTest | Run correlationTest, based on... |
| scaleBranches | Scale branch lengths to represent either mutations or... |
| stitchRegions | stitchRegions Similar to stitchVDJ but with segment IDs... |
| stitchVDJ | stitchVDJ combines germline gene segments to a single string |
| 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 |
| TimeTrees | Example Ig lineage trees sampled over time. |
| treesToPDF | Simple function for plotting a lot of trees into a pdf |
| writeLineageFile | Write lineage file for IgPhyML use |
