create_alignment: Takes an airr clone object and returns BEAST2 Alignment xml...
In dowser: B Cell Receptor Phylogenetics Toolkit

View source: R/TimeTreesFunctions.R

create_alignment

R Documentation

Takes an airr clone object and returns BEAST2 Alignment xml of the sequences

Description

Takes an airr clone object and returns BEAST2 Alignment xml of the sequences

Usage

create_alignment(clone, id, include_germline_as_tip)

Arguments

`clone`	an `airrClone` object
`id`	unique identifer for this analysis
`include_germline_as_tip`	include the germline as a tip in the alignment?

Value

String of BEAST2 Alignment and TaxonSet xml

dowser documentation built on Nov. 5, 2025, 6:36 p.m.

dowser index

Package overview README.md Building trees with paired heavy and light chain data Build Lineage Trees Build Time Trees Using TyCHE and BEAST Discrete Trait Analysis Measurable evolution Plotting Lineage Trees Quickstart Reconstruct Clonal Germlines Reconstruct Intermediate Sequences Build B cell lineage trees Building trees with paired heavy and light chain data Build Time Trees Using TyCHE and BEAST Detect ongoing B cell evolution Discrete trait analysis Dowser: Simple lineage tree construction Plot B cell lineage trees Reconstruct clonal germline sequences Reconstruct intermediate sequences Using data from non-B cells

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