basecomp

basecomp-methods

basecomp,Dna-method

Calculates base composition of <code>Dna</code> object.

DNA ANALYSIS

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix.  This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

Caner Aktas

haplotypes

Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony

basecomp-methods function

<dl> <dt>x</dt>
<dd>an object of class <code>Dna</code>.</dd> 
</dl>

Arguments

<dl>
<dt><code>signature(x = "Dna")</code></dt>
<dd>calculates base composition of <code>Dna</code> object.</dd>
</dl>

Methods

Calculates base composition — basecomp-methods

<dl>

 <dt>x</dt>
<dd>an object of class <code>Dna</code>.</dd>

 
</dl>

<dl>


<dt><code>signature(x = "Dna")</code></dt>
<dd>calculates base composition of <code>Dna</code> object.</dd>


</dl>

basecomp-methods: Calculates base composition

Description

Usage

Value

Arguments

Methods

Examples