Imports: quadprog, igraph (>= 0.6), Matrix, parallel, nnls

Imports: quadprog, igraph (>= 0.6), Matrix, fastmatch

Suggests: parallel, rgl, seqLogo, seqinr, xtable, flashClust, phytools

Imports: quadprog, igraph (>= 0.6), Matrix, parallel, nnls, methods,
Suggests: testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr

Authors@R: c(person("Klaus", "Schliep", email="klaus.schliep@gmail.com", role = c("aut", "cre")),
person("Emmanuel", "Paradis", role = c("aut")),
person("Alastair", "Potts", role = c("aut")))
Imports: quadprog, igraph (>= 1.0), Matrix, parallel, nnls, methods,
utils, stats, graphics, grDevices, Biostrings
Suggests: testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr,

utils, stats, graphics, grDevices, fastmatch

person("Alastair", "Potts", role = c("aut")),
person("Michelle", "Kendall", email="m.kendall@imperial.ac.uk", role = c("ctb")))

person("Leonardo", "de Oliveira Martins", role = c("aut")),
person("Tim W.", "White", role = c("aut")),
person("Cyrill", "Stachniss", role = c("ctb")),
Imports: quadprog, igraph (>= 1.0), Matrix, parallel, methods, utils,
stats, graphics, grDevices, fastmatch, magrittr, Rcpp (>=

Title: Phylogenetic Reconstruction and Analysis
Description: Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation (Schliep 2011). Offers methods for tree comparison,
model selection and visualization of phylogenetic networks as described in
Imports: digest, fastmatch, generics, graphics, grDevices, igraph (>=
1.0), Matrix, methods, parallel, quadprog, Rcpp, stats, utils
Suggests: Biostrings, knitr, magick, prettydoc, rgl, rmarkdown, seqinr,

Description: Package contains methods for estimation of phylogenetic trees and
networks using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation. Allows to compare trees, models selection and offers
visualizations for trees and split networks.

Suggests: testthat, seqinr, xtable, rgl, knitr, rmarkdown, Biostrings

Authors@R: c(person("Klaus", "Schliep", email="klaus.schliep@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2941-0161")),
person("Emmanuel", "Paradis", role = c("aut"), comment = c(ORCID = "0000-0003-3092-2199")),
person("Leonardo", "de Oliveira Martins", role = c("aut"), comment = c(ORCID = "0000-0001-5247-1320")),
person("Michelle", "Kendall", email="m.kendall@imperial.ac.uk", role = c("ctb")),
person("Keren", "Halabi", role = c("ctb")),
person("Richel", "Bilderbeek", role = c("ctb")))
Suggests: testthat, vdiffr, seqinr, xtable, rgl, knitr, rmarkdown,