seqStat

Utility that produces a table giving summary statistics for a `DNAbin'
object.

utilities

Barcoding

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

seqStat function

<dl><dt>DNAbin</dt>
<dd>Alignment of class `DNAbin'.</dd>
<dt>thresh</dt>
<dd>Threshold sequence length. Default of 500 (minimum length for
official DNA barcodes).</dd></dl>

Arguments

Rupert Collins &lt;rupertcollins@gmail.com&gt;

Author

Sequence statistics — seqStat

<dl>

<dt>DNAbin</dt>
<dd>Alignment of class `DNAbin'.</dd>


<dt>thresh</dt>
<dd>Threshold sequence length. Default of 500 (minimum length for
official DNA barcodes).</dd>

</dl>

seqStat: Sequence statistics

Description

Usage

Value

Arguments

Author

Details

Examples