makeModelFile

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

makeModelFile function

<dl><dt>file</dt>
<dd>model file name to write.</dd>
<dt>states</dt>
<dd>vector of states to include in model.</dd>
<dt>constraints</dt>
<dd>constraints to add to model.</dd>
<dt>exceptions</dt>
<dd>vector of comma-separated states that are 
exceptions to constraints</dd></dl>

Arguments

Make a parsimony model file — makeModelFile

<dl>

<dt>file</dt>
<dd>model file name to write.</dd>


<dt>states</dt>
<dd>vector of states to include in model.</dd>


<dt>constraints</dt>
<dd>constraints to add to model.</dd>


<dt>exceptions</dt>
<dd>vector of comma-separated states that are 
exceptions to constraints</dd>

</dl>

Make a parsimony model file

makeModelFile: Make a parsimony model file

Description

Usage

Value

Arguments

Details

See Also