are_mrca_align_ids_in_fasta

Determine if the MRCA priors' alignment IDs are present in the FASTA files

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.

Richèl J.C. Bilderbeek

beautier

'BEAUti' from R

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Olivier Roy

Jana Riederer

are_mrca_align_ids_in_fasta function

<dl><dt>mrca_prior</dt>
<dd>a Most Recent Common Ancestor prior,
as returned by <code>create_mrca_prior</code></dd>
<dt>fasta_filename</dt>
<dd>a FASTA filename.
Use <code>get_fasta_filename</code> to obtain a testing FASTA filename.
Note that BEAST2 also supports missing data,
by using a dash (<code>-</code>) or question mark (<code>?</code>)
as a sequence.</dd></dl>

Arguments

Author

Determine if the MRCA priors' alignment IDs are present in the FASTA files — are_mrca_align_ids_in_fasta

<dl>

<dt>mrca_prior</dt>
<dd>a Most Recent Common Ancestor prior,
as returned by <code>create_mrca_prior</code></dd>


<dt>fasta_filename</dt>
<dd>a FASTA filename.
Use <code>get_fasta_filename</code> to obtain a testing FASTA filename.
Note that BEAST2 also supports missing data,
by using a dash (<code>-</code>) or question mark (<code>?</code>)
as a sequence.</dd>

</dl>

Determine if the MRCA priors' alignment IDs are present in the FASTA files

are_mrca_align_ids_in_fasta: Determine if the MRCA priors' alignment IDs are present in the FASTA files

Description

Usage

Value

Arguments

Author