API for dowser
B Cell Receptor Phylogenetics Toolkit

Global functions
.onAttach	Source code
BiopsyTrees	Man page
ExampleAirr	Man page
ExampleAirrTyCHE	Man page
ExampleClones	Man page
ExampleDbChangeo	Man page
ExampleMixedClones	Man page
ExampleMixedDb	Man page
IsotypeTrees	Man page
TimeTrees	Man page
airrClone	Man page
airrClone-class	Man page
bootstrapClones	Source code
bootstrapTrees	Man page Source code
buildBeast	Man page Source code
buildClonalGermline	Man page Source code
buildGermline	Man page Source code
buildIgphyml	Man page Source code
buildPML	Man page Source code
buildPhylo	Man page Source code
buildPratchet	Man page Source code
buildRAxML	Man page Source code
calcRF	Man page Source code
checkDivergence	Man page Source code
cleanAlignment	Source code
cloneToFasta	Source code
collapseNodes	Man page Source code
colorTrees	Man page Source code
combineColors	Source code
condenseTrees	Man page Source code
consensus_tree	Source code
correlationTest	Man page Source code
createGermlines	Man page Source code
create_MRCA_prior_germline	Man page Source code
create_MRCA_prior_observed	Man page Source code
create_alignment	Man page Source code
create_height_prior	Man page Source code
create_max_height_prior	Man page Source code
create_root_freqs	Man page Source code
create_starting_tree	Man page Source code
create_traitset	Man page Source code
dfToFasta	Man page Source code
downsampleClone	Man page Source code
dowser	Man page
dowser-package	Man page
exportTrees	Man page Source code
findSwitches	Man page Source code
formatClones	Man page Source code
getAllSeqs	Man page Source code
getBootstraps	Man page Source code
getDivergence	Man page Source code
getGermline	Man page Source code
getNodeSeq	Man page Source code
getPalette	Man page Source code
getSeq	Man page Source code
getSkylines	Man page Source code
getSubTaxa	Man page Source code
getSubclones	Man page Source code
getTimeTrees	Man page Source code
getTimeTreesIterate	Man page Source code
getTrees	Man page Source code
makeAirrClone	Man page Source code
makeModelFile	Man page Source code
makeSkyline	Man page Source code
makeTrees	Source code
maskCodons	Man page Source code
maskSequences	Man page Source code
matching_function_parallel	Source code
plotSkylines	Man page Source code
plotTrees	Man page Source code
processClones	Source code
readBEAST	Man page Source code
readFasta	Man page Source code
readIMGT	Man page Source code
readLineages	Man page Source code
readModelFile	Man page Source code
readSwitches	Source code
reconIgPhyML	Man page Source code
rerootTree	Man page Source code
resolveLightChains	Man page Source code
resolvePolytomies	Man page Source code
runCorrelationTest	Man page Source code
sampleCloneMultiGroup	Man page Source code
sampleClones	Man page Source code
scaleBranches	Man page Source code
splits_func	Source code
stitchRegions	Man page Source code
stitchVDJ	Man page Source code
stopCodonCheck	Man page Source code
testPS	Man page Source code
testSC	Man page Source code
testSP	Man page Source code
treesToPDF	Man page Source code
writeCloneSequences	Man page Source code
writeLineageFile	Man page Source code
write_clone_to_xml	Man page Source code
write_clones_to_xmls	Man page Source code