Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

TreeSearch: morphological phylogenetic analysis in R

View ORCID ProfileMartin R. Smith
doi: https://doi.org/10.1101/2021.11.08.467735
Martin R. Smith
Department of Earth Sciences, Durham University, Lower Mountjoy, Durham, DH1 3LE, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martin R. Smith
  • For correspondence: martin.smith@durham.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

TreeSearch is an R package for phylogenetic analysis, optimized for morphological datasets. Tree search may be conducted using 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 summarizing 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • martin.smith{at}durham.ac.uk

  • Update installation instructions, improve figure 1, and copyedit text

  • https://github.com/ms609/TreeSearch/

  • https://dx.doi.org/10.5281/zenodo.1042590

  • https://ms609.github.io/TreeSearch/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted January 25, 2022.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
TreeSearch: morphological phylogenetic analysis in R
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
TreeSearch: morphological phylogenetic analysis in R
Martin R. Smith
bioRxiv 2021.11.08.467735; doi: https://doi.org/10.1101/2021.11.08.467735
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
TreeSearch: morphological phylogenetic analysis in R
Martin R. Smith
bioRxiv 2021.11.08.467735; doi: https://doi.org/10.1101/2021.11.08.467735

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3579)
  • Biochemistry (7526)
  • Bioengineering (5486)
  • Bioinformatics (20703)
  • Biophysics (10261)
  • Cancer Biology (7939)
  • Cell Biology (11585)
  • Clinical Trials (138)
  • Developmental Biology (6574)
  • Ecology (10145)
  • Epidemiology (2065)
  • Evolutionary Biology (13556)
  • Genetics (9502)
  • Genomics (12796)
  • Immunology (7888)
  • Microbiology (19460)
  • Molecular Biology (7618)
  • Neuroscience (41917)
  • Paleontology (307)
  • Pathology (1253)
  • Pharmacology and Toxicology (2182)
  • Physiology (3253)
  • Plant Biology (7011)
  • Scientific Communication and Education (1291)
  • Synthetic Biology (1942)
  • Systems Biology (5410)
  • Zoology (1108)