Identify clonal clusters | Obtain IMGT-gapped sequences | Construct clonal germlines

Reading AIRR Rearrangement sequencing data files | scRepertoire and Dowser compatability | Saving and loading Dowser objects in AIRR Clone JSON format | Saving and loading Dowser objects as RDS | Exporting trees in Newick format | Exporting and reading sequences as FASTA | Making and saving tree plots

Building Time Trees | Requirements | For Mac and Windows machines, we recommend: | For Linux machines, we recommend running: | Download and set up XML templates | Setting up data | Estimating the GC clock rate | Run getTimeTreesIterate with a TyCHE template | Visualize the results

Resolve light chains | Reconstruct germlines | Format clones | Building trees

Date randomization test | Set up data structures and trees | Perform date randomization test | Plot trees

Removing partial sequences | Removing "comb" artifacts | Simulating a comb artifact | Removing comb artifacts | Choosing parameters | Recommended order

Format clones | Build maximum parsimony trees | Build maximum likelihood trees | Build IgPhyML B cell trees | Building maximum likelihood trees with multiple partitions

Discrete trait statistics | Caveats and interpreting results | Setting up IgPhyML | Set up data structures and trees | Visualize maximum parsimony trait reconstruction | Discrete trait analysis with fixed trees | Accounting for uncertainty in tree topology | Within and between lineage permutations | Controlling false positive rate through downsampling | Incorporating switching constraints

Saving sequences to a file

Basic plotting | Plotting metadata | Using ggtree and ggplot functions | Editing all trees at once | Saving trees to a file