validate_tree

This function checks whether the input is a valid phylogenetic tree, either as a character string in Newick format
or as an object of class <code>phylo</code> from the <code>ape</code> package. If the input is a Newick string, it is parsed into
a <code>phylo</code> object. The function also ensures that the tree contains at least two tips.

DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the methylation states at single cytosine positions as well as simultaneous changes of methylation
frequencies in genomic structures like CpG islands.

Sara Castillo Vicente

MethEvolSIM

Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies

Dirk Metzler

validate_tree function

<dl><dt>tree</dt>
<dd>A phylogenetic tree in Newick format (as a character string) or an object of class <code>phylo</code> from the <code>ape</code> package.<ul>
<li>If the input is a character string, it must follow the Newick format (e.g., <code>"((tip_1:1,tip_2:1):5,tip_3:6);"</code>).</li>
<li>If an object of class <code>phylo</code> is provided, it should be a valid phylogenetic tree.</li>
</ul></dd></dl>

Arguments

Validate and Parse a Phylogenetic Tree — validate_tree

<dl>

<dt>tree</dt>
<dd>A phylogenetic tree in Newick format (as a character string) or an object of class <code>phylo</code> from the <code>ape</code> package.<ul>
<li>If the input is a character string, it must follow the Newick format (e.g., <code>"((tip_1:1,tip_2:1):5,tip_3:6);"</code>).</li>
<li>If an object of class <code>phylo</code> is provided, it should be a valid phylogenetic tree.</li>
</ul></dd>

</dl>

validate_tree: Validate and Parse a Phylogenetic Tree

Description

Usage

Value

Arguments

Details