Dear R users, TreeSearch is an R package for phylogenetic analysis, optimized for morphological datasets. Tree search may be conducted using under equal or implied step weights with an explicit (albeit inexact) allowance for inapplicable character entries, avoiding some of the pitfalls inherent in standard parsimony methods. Profile parsimony and user-specified optimality criteria are supported.
A graphical interface, which requires no familiarity with R, is designed to help a user to improve the quality of datasets through critical review of underpinning character codings; and to obtain additional information from results by identifying and summarising clusters of similar trees, mapping the distribution of trees, and removing ‘rogue’ taxa that obscure underlying relationships. Taken together, the package aims to support methodological rigour at each step of data collection, analysis, and the exploration of phylogenetic results. A stable release of TreeSearch is now on CRAN: https://CRAN.R-project.org/package=TreeSearch An introduction to the package is provided in the vignette: https://ms609.github.io/TreeSearch/articles/tree-search.html Further details are in the BioRχiv preprint: https://www.biorxiv.org/content/10.1101/2021.11.08.467735 Regards, Martin -- *Dr. Martin R. Smith* Associate Professor in Palaeontology Durham University Department of Earth Sciences Mountjoy Site, South Road, Durham, DH1 3LE United Kingdom *M*: +44 (0)774 353 7510 *E*: martin.sm...@durham.ac.uk smithlabdurham.github.io twitter.com/PalaeoSmith My working days are Monday–Thursday. The information in this e-mail and any attachments is co...{{dropped:7}} ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.