Phylogenetic Tree Search Using Custom Optimality Criteria
c(person("Martin R.", 'Smith',
email="martins@gmail.com",
role=c("aut", "cre", "cph"),
comment=c(ORCID = "0000-0001-5660-1727")),
person(given = "Emmanuel", family="Paradis",
role = c("cph")),
person(given = "Klaus", family="Schliep",
role = c("cph"))
)
Incorporates C code from the ape and phangorn packages by
Emmanuel Paradis and Klaus Schliep. Code is copied rather than
linked in the absence of a suitable R interface.
Searches for phylogenetic trees that are optimal using a user-defined criterion. Employed in Brazeau Guillerme and Smith (2017) <doi:10.1101/209775>.
Martin R. Smith [aut, cre, cph] (0000-0001-5660-1727),
Emmanuel Paradis [cph],
Klaus Schliep [cph]

c(person("Martin R.", 'Smith',
email="martins@gmail.com",
role=c("aut", "cre", "cph"),
comment=c(ORCID = "0000-0001-5660-1727")),
person(given = "Emmanuel", family="Paradis",
role = c("cph")),
person(given = "Martin", family="Brazeau",
role = c("cph"))
)
Incorporates C code from: ape by Emmanuel Paradis; Morphy
Phylogenetic Library by Martin Brazeau
<https://github.com/mbrazeau/MorphyLib> (GPL3)
Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau Guillerme and Smith (2017) <doi:10.1101/209775>.
ape (>= 5.0), memoise, phangorn (>= 2.2.1), R.cache, Rdpack,
stats
Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph],
Martin Brazeau [cph]

c(person("Martin R.", 'Smith',
email="martin.smith@durham.ac.uk",
role=c("aut", "cre", "cph"),
comment=c(ORCID = "0000-0001-5660-1727")),
person(given = "Emmanuel", family="Paradis",
role = c("cph")),
person(given = "Martin", family="Brazeau",
role = c("cph"))
)
ape (>= 5.0), colorspace, gmp, memoise, phangorn (>= 2.2.1),
R.cache, Rdpack, stats

c(person("Martin R.", 'Smith',
email="martin.smith@durham.ac.uk",
role=c("aut", "cre", "cph"),
comment=c(ORCID = "0000-0001-5660-1727")),
person(given = "Emmanuel", family="Paradis", role = c("cph"),
comment = c(ORCID = "0000-0003-3092-2199")),
person(given = "Klaus", family="Schliep", role = c("cph"),
comment = c(ORCID = "0000-0003-2941-0161")),
person(given = "Martin", family="Brazeau", role = c("cph"),
comment = c(ORCID = "0000-0002-0650-1282"))
)
Incorporates C/C++ code from: ape by Emmanuel Paradis;
phangorn by Klaus Scheip <doi:10.1093/bioinformatics/btq706>;
Morphy Phylogenetic Library by Martin Brazeau
<https://github.com/mbrazeau/MorphyLib> (GPL3)
Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
(2019) <doi:10.1093/sysbio/syy083>.
ape (>= 5.0), colorspace, gmp, memoise, phangorn (>= 2.2.1),
R.cache, Rcpp, Rdpack, stats