checkDNA

This functions counts the number of bases in an alignment that are composed
of missing data.

utilities

Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.

Rupert Collins

spider

Species Identity and Evolution in R

Samuel Brown

Stephane Boyer

Marie-Caroline Lefort

Jagoba Malumbres-Olarte

Cor Vink

Rob Cruickshank

checkDNA function

<dl><dt>DNAbin</dt>
<dd>A DNA alignment of class `DNAbin'.</dd>
<dt>gapsAsMissing</dt>
<dd>Logical. Should gaps (coded as '-') be considered
missing bases? Default of TRUE.</dd></dl>

Arguments

Samuel Brown &lt;s_d_j_brown@hotmail.com&gt;

Author

Check a DNA alignment for missing data — checkDNA

<dl>

<dt>DNAbin</dt>
<dd>A DNA alignment of class `DNAbin'.</dd>


<dt>gapsAsMissing</dt>
<dd>Logical. Should gaps (coded as '-') be considered
missing bases? Default of TRUE.</dd>

</dl>

checkDNA: Check a DNA alignment for missing data

Description

Usage

Value

Arguments

Author

Details

Examples