Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001)
It extends the basic functionality available in phangorn, with a view to making tree search faster and more efficient, and allowing user-defined optimality criteria to be employed.
Implied weighting and heuristic searches such as the Parsimony Ratchet are implemented (function:
Browse the vignettes (with
vignette(package = "TreeSearch") to get started.
Install and load the library from CRAN as follows:
If you're feeling brave, you can install the development version thus:
TreeSearch allows the implementation of various optimality criteria, including
It is also possible to specify bespoke optimality criteria.
Brazeau, M. D., Guillerme, T. and Smith, M. R. 2017. Morphological phylogenetic analysis with inapplicable data. BioRχiv. doi:10.1101/209775
D. P. Faith, J. W. H. Trueman, Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50, 331–350 (2001). doi:10.1080/10635150118627
Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi:10.2307/2412182
RootTreefunction allows rooting of tree on incompletely specified or single-taxon outgroup
AllTBRreturns all trees one TBR rearrangement away
TBRMovesreports all possible TBR rearrangements
Jackknifeconducts Jackknife resampling
SplitFrequencyreports frequency of clades in a forest
SupportColourallows visual marking of support values
ApeTimereports the creation date of an ape-exported tree
SortTreeflips nodes into a consistent left-right order
IWRatchetConsensusnow relays concavity value to subsequent functions
ReadCharactersreturns labels for all characters and states if
character_num = NULL