The phalen package contains (1) clustering and
partitioning algorithms; (2) penalty functions for numeric
vectors; (3) a ranking function; and (4) color palettes and
functions.

Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)

parallel, seqLogo, rgl, seqinr, xtable, flashClust

parallel, seqLogo, seqinr, xtable, flashClust, phytools

quadprog, igraph (>= 0.6), Matrix, fastmatch, parallel, rgl

Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
quadprog, igraph (>= 0.6), Matrix, fastmatch, parallel, nnls
seqLogo, seqinr, xtable, flashClust, rgl, knitr

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

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

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

quadprog, igraph (>= 0.6), Matrix, parallel, nnls, methods,
utils, stats, graphics, grDevices
testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr

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")))
quadprog, igraph (>= 1.0), Matrix, parallel, nnls, methods,
utils, stats, graphics, grDevices, Biostrings
testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr,
msa
Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]

quadprog, igraph (>= 1.0), Matrix, parallel, nnls, methods,
utils, stats, graphics, grDevices
testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr,
rmarkdown, Biostrings

quadprog, igraph (>= 1.0), Matrix, parallel, nnls, methods,
utils, stats, graphics, grDevices, fastmatch

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")),
person("Michelle", "Kendall", email="m.kendall@imperial.ac.uk", role = c("ctb")))
Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut],
Michelle Kendall [ctb]