Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony
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.
methods, stats, utils, network, sna, ape, phangorn,
pegas,plotrix

methods, stats, utils, network, sna, ape, phangorn,plotrix

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 infering 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.
methods, stats, utils, network, sna, ape, phangorn, pegas,
plotrix

person("Paul", "Carteron", , "carteronpaul@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-6942-6662"))
Interface to easily access the National Institute of
Geographic and Forestry Information open-source data for any area of
interest in France via the expert web service
<https://geoservices.ign.fr/services-web-experts>.
dplyr, httr, magrittr, sf, stars, stringr, tidyr, xml2
covr, knitr, rmarkdown, testthat (>= 3.0.0), tmap, vcr (>=
0.6.0), webmockr
Paul Carteron [aut, cre] (<https://orcid.org/0000-0002-6942-6662>)