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Related Experiment Video

Updated: Jun 24, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Using PhyloSuite for molecular phylogeny and tree-based analyses.

Chuan-Yu Xiang¹, Fangluan Gao², Ivan Jakovlić¹

¹State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology Lanzhou University Lanzhou China.

|June 13, 2024

Summary

This summary is machine-generated.

PhyloSuite simplifies complex multilocus phylogenetic analysis for researchers. This user-friendly software integrates essential tools, making phylogenomic reconstruction more accessible and efficient, especially for organelle-based studies.

Keywords:

annotation concatenation iTOL loci multiple‐sequence alignment partitioning trimming

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Last Updated: Jun 24, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Multilocus phylogenetic analysis is crucial in the genomics era.
Navigating numerous software programs for phylogenomic reconstruction is challenging for less experienced researchers.
PhyloSuite aims to simplify this process by integrating multiple software tools.

Purpose of the Study:

To provide a comprehensive protocol for conducting multilocus phylogenetic analyses using PhyloSuite.
To introduce PhyloSuite v1.2.3, highlighting bug fixes, optimizations, and new tree-based analysis functions.
To assist researchers, particularly those focusing on organelle-based phylogenies, in quick-starting their analyses.

Main Methods:

Utilizing PhyloSuite's graphical user interface (GUI) for an integrated phylogenetic pipeline.
Implementing step-by-step guidance covering background, rationale, and operational procedures for each analysis step.
Employing new functions in PhyloSuite v1.2.3 for advanced tree-based analyses.

Main Results:

PhyloSuite v1.2.3 offers a streamlined workflow for multilocus phylogenetic reconstruction.
New functionalities include signal-to-noise calculation, saturation analysis, and spurious species identification.
The protocol facilitates efficient execution of phylogenetic and tree-based analyses.

Conclusions:

PhyloSuite significantly lowers the barrier to entry for complex multilocus phylogenetic analyses.
The software and accompanying protocol empower researchers to conduct advanced phylogenomic studies more effectively.
This resource is particularly valuable for organelle genomics and researchers new to phylogenetics.