[R-pkgs] new package RFLPtools

From: Dr. Matthias Kohl <Matthias.Kohl_at_stamats.de>
Date: Sat, 20 Feb 2010 09:31:35 +0100


The new package RFLPtools is available on CRAN.

RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further analysis of similarities of nucleotide sequences derived from pairwise sequence alignments (e.g.\ derived from standalone BLAST). Additionally, functions to check the data quality of molecular fingerprints are available. To identify the organisms represented by the extracted fragment patterns (e.g.\ RFLP genotypes), RFLPtools includes a function to compare samples with fragment patterns stored in a reference dataset, from which the taxonomic affiliations are already known. To identify unknown samples in scientific projects, DNA sequences are used, and the gained DNA sequences are compared to existing sequence data via alignments tools, as standalone BLAST.
RFLPtools offers tools to generate groups based on tabular report files of sequence comparison of pairwise nucleotide sequence alignment.

To get a first impression try:

vignette("RFLPtools")

as well as

library(RFLPtools)
example("RFLPplot")
example("RFLPrefplot")

Best regards,
Fabienne
Alexandra
Matthias

-- 
Dr. Matthias Kohl
www.stamats.de

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Received on Sun 21 Feb 2010 - 08:51:04 EST

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