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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