knitr, Rcpp, rmarkdown, shiny, testthat, xlsx

ape (>= 5.0), clue, colorspace, 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 = "Martin", family="Brazeau", role = c("cph"),
comment = c(ORCID = "0000-0002-0650-1282"))
)
Incorporates C/C++ code from Morphy Phylogenetic Library by
Martin Brazeau <https://github.com/mbrazeau/MorphyLib> (GPL3)
Searches for phylogenetic trees that are optimal using a
user-defined criterion.
Handles inapplicable data using the algorithm of
Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.
Implements Profile Parsimony (Faith and Trueman, 2001)
<doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969)
<doi:10.2307/2412182>.
ape (>= 5.0), phangorn (>= 2.2.1), R.cache, Rdpack, stats,
TreeTools

ape (>= 5.0), phangorn (>= 2.2.1), R.cache, Rdpack, stats,
TreeTools (>= 1.0.0)

Search for phylogenetic trees that are optimal using a
user-defined criterion.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and
Smith (2019) <doi:10.1093/sysbio/syy083> using the "Morphy" library.
Implements Profile Parsimony (Faith and Trueman, 2001)
<doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969)
<doi:10.2307/2412182>.
ape (>= 5.1.2), cli (>= 3.0), cluster, fastmatch (>= 1.1.3),
future, phangorn (>= 2.2.1), promises, protoclust, Rcpp, Rdpack
(>= 0.7), Rogue (> 1.0.0), shiny, shinyjs, stats, TreeDist (>
2.0.3), TreeTools (>= 1.5.0),
knitr, rmarkdown, Quartet, testthat, vdiffr (>= 1.0.0),

Phylogenetic Analysis with Morphological Data
Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
ape (>= 5.6), cli (>= 3.0), cluster, fastmatch (>= 1.1.3),
future, phangorn (>= 2.2.1), promises, protoclust, Rcpp, Rdpack
(>= 0.7), Rogue (> 2.0.0), shiny (>= 1.6.0), shinyjs, stats,
TreeDist (>= 2.3.0), TreeTools (>= 1.6.0),
knitr, Quartet, rmarkdown, spelling, testthat, vdiffr (>=
1.0.0),