reconIgPhyML

<code>reconIgPhyML</code> IgPhyML parsimony reconstruction function

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

reconIgPhyML function

<dl><dt>file</dt>
<dd>IgPhyML lineage file (see writeLineageFile)</dd>
<dt>modelfile</dt>
<dd>File specifying parsimony model</dd>
<dt>id</dt>
<dd>id for IgPhyML run</dd>
<dt>igphyml</dt>
<dd>location of igphyml executable</dd>
<dt>mode</dt>
<dd>return trees or count switches? (switches or trees)</dd>
<dt>type</dt>
<dd>get observed switches or permuted switches?</dd>
<dt>nproc</dt>
<dd>cores to use for parallelization</dd>
<dt>quiet</dt>
<dd>amount of rubbish to print</dd>
<dt>rm_files</dt>
<dd>remove temporary files?</dd>
<dt>rm_dir</dt>
<dd>remove temporary directory?</dd>
<dt>states</dt>
<dd>states in parsimony model</dd>
<dt>palette</dt>
<dd>deprecated</dd>
<dt>resolve</dt>
<dd>level of polytomy resolution. 0=none, 
1=maximum parsimony, 2=maximum ambiguity</dd>
<dt>rseed</dt>
<dd>random number seed if desired</dd>
<dt>force_resolve</dt>
<dd>continue even if polytomy resolution fails?</dd>
<dt>...</dt>
<dd>additional arguments</dd></dl>

Arguments

Do IgPhyML maximum parsimony reconstruction — reconIgPhyML

<dl>

<dt>file</dt>
<dd>IgPhyML lineage file (see writeLineageFile)</dd>


<dt>modelfile</dt>
<dd>File specifying parsimony model</dd>


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


<dt>igphyml</dt>
<dd>location of igphyml executable</dd>


<dt>mode</dt>
<dd>return trees or count switches? (switches or trees)</dd>


<dt>type</dt>
<dd>get observed switches or permuted switches?</dd>


<dt>nproc</dt>
<dd>cores to use for parallelization</dd>


<dt>quiet</dt>
<dd>amount of rubbish to print</dd>


<dt>rm_files</dt>
<dd>remove temporary files?</dd>


<dt>rm_dir</dt>
<dd>remove temporary directory?</dd>


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


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


<dt>resolve</dt>
<dd>level of polytomy resolution. 0=none, 
1=maximum parsimony, 2=maximum ambiguity</dd>


<dt>rseed</dt>
<dd>random number seed if desired</dd>


<dt>force_resolve</dt>
<dd>continue even if polytomy resolution fails?</dd>


<dt>...</dt>
<dd>additional arguments</dd>

</dl>

reconIgPhyML: Do IgPhyML maximum parsimony reconstruction

Description

Usage

Value

Arguments