This package provides integration for the maximum parsimony phylogenetic software TNT (Goloboff et al. 2008, Goloboff and Catalano 2016, Goloboff and Morales 2023), in R. It interfaces with a locally installed copy of the TNT command line executable and provides functions for performing branch swapping, parsimony ratchet and driven (i.e., "New Technology") searches. Each tree search function automatically returns a set of trees for visualisation or use with other R packages.
nitro is not currently available on CRAN and must be installed directly from
this repository. Firstly, install the treeio package, which is made available
via Bioconductor and which can be installed using
the R package BiocManager:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("treeio")Then install nitro from this repository using devtools:
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("paravian/nitro")nitro currently has R6 configuration option classes for the following tree
analysis methods implemented by TNT:
BranchSwappingOptions),
ratcheting (RatchetOptions), branch breaking (BranchBreakingOptions),
sectorial searches (ConstrainedSectorialSearchOptions,
ExclusiveSectorialSearchOptions, RandomSectorialSearchOptions), drifting
(TreeDriftingOptions), fusing (TreeFusingOptions), hybridizing
(TreeHybridizingOptions) and driven (i.e., "new technology") searches
(DrivenSearchOptions);BootstrapOptions, JackknifeOptions,
SymmetricResamplingOptions)BranchSupportOptions)ImpliedWeightingOptions)MonophylyConstraintOptions)If you have used nitro in a publication and have found it useful, please
consider citing it alongside TNT as follows:
Birch, S. 2023. nitro: Integration of TNT in R. GitHub repository: https://github.com/paravian/nitro.
Goloboff, P.A., Farris, J.S., Nixon, K.C., 2008. TNT, a free program for phylogenetic analysis. Cladistics 24, 774–786. https://doi.org/10.1111/j.1096-0031.2008.00217.x
Goloboff, P.A., Catalano, S.A., 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32, 221–238. https://doi.org/10.1111/cla.12160
Goloboff, P.A., Morales, M.E., 2023. TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel. Cladistics 39, 144–153. https://doi.org/10.1111/cla.12524
TNT is made available thanks to a subsidy from the Willi Hennig Society.