guoyi.run: One-step TNT script for maximum parsimony phylogenetic

[Guoyi Zhang]

Hello everyone

I am sharing a new TNT script, guoyi.run

This tool is incredibly useful for anyone working with morphological phylogenetic analysis even molecular phylogenetics. It aims to make maximum parsimony phylogenetic analyses more reproducible and has already been adopted in numerous studies in entomology and palaeontology.

It provides a one-step TNT pipeline that supports multiple weighting schemes (equal, implied, and extended implied), customizable K values, consensus tree type selection, and resampling methods such as Bremer, bootstrap, and jackknife. It also automatically generates svg files and output files compatible with WinClada and FigTree. The entire analysis runs with a single command and intelligently adjusts tree search strategies based on dataset size.

Huge thanks to Pablo Goloboff, the author of TNT, for his encouragement and valuable comments.

Paper: https://doi.org/10.11646/zootaxa.5642.1.10

Best regards

Guoyi

[Guoyi Zhang]

For anyone who wants to get a copy of the PDF, feel free to look at my researchgate and website

https://www.researchgate.net/profile/Guoyi-Zhang

https://malacology.net/about/

Best regards

Guoyi

[Jonathan Liria]

Hi Gouyi

Thanks!!!

JL

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Researchgate ; Scopus ; Google Scholar ; Linkedin ; Orcid ; Publons

[Serdar Sönmez]

Hello Guoyi,

Thank you very much for sharing the script and the paper

Best

Jonathan Liria <jonatha...@gmail.com>, 28 May 2025 Çar, 15:52 tarihinde şunu yazdı:

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Prof. Dr. Serdar SÖNMEZ

Adıyaman Üniversitesi Fen Edebiyat Fakültesi Biyoloji Bölümü

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[Anderson da Silva Nascimento]

Hello, Guoyi!
Thanks for the script
I try to run it and this appears:

Should i do something else before?
Sorry for the doubt, I've gone through your paper, but I’m still having a bit of trouble wrapping my head around the programming part.

Best regards,

[Zhang Guoyi]

I made a tutorial for that

https://youtu.be/mU0KcbEPgcE

Best regards 

Guoyi

Guoyi Zhang

Personal Web | ORCID

School of Biological, Earth and Environmental Sciences

University of New South Wales

Australian Museum Research Institute

Australian Museum

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From: tnt-tree-analysis-u...@googlegroups.com <tnt-tree-analysis-u...@googlegroups.com> on behalf of Anderson da Silva Nascimento <anders...@gmail.com>
Sent: Saturday, April 4, 2026 8:38:55 AM
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Subject: Re: guoyi.run: One-step TNT script for maximum parsimony phylogenetic

 

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