Taxacom: A one-step TNT scipt for MP phylogenetics

[Kuoi Zhang]

Hello everyone

I am sharing a new TNT script, guoyi.run, for one-step MP phylogenetics

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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.11646%2Fzootaxa.5642.1.10&data%7C02%7Ctaxacom%40lists.ku.edu%7C1e796e7373774924f46008dd9e7876af%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638840962427793531%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ZM2CGUevQRcWE1opGm3bNHjhhEtIjncivRmG0BXLdkw%3D&reserved=0

Best regards
Guoyi

Guoyi Zhang (she/her), MRes, PhD candidate
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School of Biological, Earth and Environmental Sciences
University of New South Wales
Australian Museum Research Institute
Australian Museum