readLineages

Read in all trees from a lineages file

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

readLineages function

<dl><dt>file</dt>
<dd>IgPhyML lineage file</dd>
<dt>states</dt>
<dd>states in parsimony model</dd>
<dt>palette</dt>
<dd>deprecated</dd>
<dt>run_id</dt>
<dd>id used for IgPhyML run</dd>
<dt>quiet</dt>
<dd>avoid printing rubbish on screen?</dd>
<dt>append</dt>
<dd>string appended to fasta files</dd>
<dt>format</dt>
<dd>format of input file with trees</dd>
<dt>type</dt>
<dd>Read in parsimony reconstructions or ancestral sequence
reconstructions? "jointpars" reads in parsimony states, 
others read in sequences in internal nodes</dd></dl>

Arguments

Read in all trees from a lineages file — readLineages

<dl>

<dt>file</dt>
<dd>IgPhyML lineage file</dd>


<dt>states</dt>
<dd>states in parsimony model</dd>


<dt>palette</dt>
<dd>deprecated</dd>


<dt>run_id</dt>
<dd>id used for IgPhyML run</dd>


<dt>quiet</dt>
<dd>avoid printing rubbish on screen?</dd>


<dt>append</dt>
<dd>string appended to fasta files</dd>


<dt>format</dt>
<dd>format of input file with trees</dd>


<dt>type</dt>
<dd>Read in parsimony reconstructions or ancestral sequence
reconstructions? "jointpars" reads in parsimony states, 
others read in sequences in internal nodes</dd>

</dl>

readLineages: Read in all trees from a lineages file

Description

Usage

Value

Arguments