plot_alignment_from_file

Plot an alignment stored as a file

Theoretical biologists are interested in measuring the extent
at which we can measure the truth. This package allows to
create a Bayesian posterior from a phylogeny that depicts
the true evolutionary relationships. The given and true phylogeny
can than be compared to the posterior phylogenies.
Richèl J. C. Bilderbeek, Giovanni Laudanno, Rampal S. Etienne (2020)
"Quantifying the impact of an inference model in Bayesian phylogenetics"
<doi:10.1111/2041-210X.13514>.

Richel Bilderbeek

pirouette

Create a Bayesian Posterior from a Phylogeny

Richèl J.C. Bilderbeek

Giovanni Laudanno

Thijs Janzen

plot_alignment_from_file function

<dl><dt>fasta_filename</dt>
<dd>name of a FASTA file.
Use get_alignment_id to get the ID of the alignment</dd>
<dt>title</dt>
<dd>the plot title
alignment_params &lt;- create_test_alignment_params()
alignment &lt;- create_tral_file(
 phylogeny = ape::rcoal(4),
 alignment_params = alignment_params
)
plot_alignment_from_file(fasta_filename = alignment_params$fasta_filename)</dd></dl>

Arguments

Plot an alignment stored as a file — plot_alignment_from_file

<dl>

<dt>fasta_filename</dt>
<dd>name of a FASTA file.
Use get_alignment_id to get the ID of the alignment</dd>


<dt>title</dt>
<dd>the plot title
alignment_params &lt;- create_test_alignment_params()
alignment &lt;- create_tral_file(
 phylogeny = ape::rcoal(4),
 alignment_params = alignment_params
)
plot_alignment_from_file(fasta_filename = alignment_params$fasta_filename)</dd>

</dl>

plot_alignment_from_file: Plot an alignment stored as a file

Description

Usage

Value

Arguments