Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL DOI Creative Commons

Hong-Yun Shang,

Kai‐Hua Jia,

Naiwei Li

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 21, 2024

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature thus frequently result discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability numerous tools for detecting ILS IH among species, many these lack effective visualization, or time-consuming, require prior predetermination. Here, we addressed shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining indices quantify IH, this can detect extent lineages with high reliability, visualize them based on gene topology patterns constructed using ASTRAL. We tested Phytop extensively both simulated real data, found that it enables users quickly conveniently estimate clarifying uncertainty. is available at https://github.com/zhangrengang/phytop expected contribute intuitive convenient inference genetic relationships future research.

Language: Английский

Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL DOI Creative Commons

Hong-Yun Shang,

Kai‐Hua Jia,

Naiwei Li

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 21, 2024

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature thus frequently result discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability numerous tools for detecting ILS IH among species, many these lack effective visualization, or time-consuming, require prior predetermination. Here, we addressed shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining indices quantify IH, this can detect extent lineages with high reliability, visualize them based on gene topology patterns constructed using ASTRAL. We tested Phytop extensively both simulated real data, found that it enables users quickly conveniently estimate clarifying uncertainty. is available at https://github.com/zhangrengang/phytop expected contribute intuitive convenient inference genetic relationships future research.

Language: Английский

Citations

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