[R-pkgs] Analysis of phylogenetic datasets in R: package "TreeSearch"

[Martin R. Smith]

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.smith using durham.ac.uk

smithlabdurham.github.io
twitter.com/PalaeoSmith

My working days are Monday–Thursday.

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