CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes.

IF 2.9 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

BMC Bioinformatics Pub Date : 2025-02-14 DOI:10.1186/s12859-025-06034-2

Peng Sun, Yu Yang, Mengjie Yuan, Qin Tang

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引用次数: 0

Abstract

Background: Over the past decade, the continuous and rapid advances in bioinformatics have led to an increasingly common use of molecular sequence comparison for phylogenetic analysis. However, the use of multi-software and cross-platform strategies has increased the complexity of phylogenetic tree estimation. Therefore, the development and application of streamlined phylogenetic analysis tools are growing in significance in the field of biology. Particularly for genomes with relatively short sequences, there is a lack of simple and integrative tools for phylogenetic analysis.

Results: In this study, we present CamlTree (Concatenated alignments maximum-likelihood tree), a user-friendly desktop software designed to simplify phylogenetic analysis for viral and mitochondrial genomes, ultimately facilitating related research. CamlTree provides a workflow including gene concatenation (or coalescence), sequence alignment, alignment optimization, and the estimation of phylogenetic trees using both maximum-likelihood (ML) and Bayesian inference (BI) methods. CamlTree was written in TypeScript and developed using the Electron framework. It offers a primarily user-friendly interface based on the React framework.

Conclusions: CamlTree software has been released for the Windows OS. It integrates several popular analysis tools to optimize and simplify the process of estimating polygenic phylogenetic trees. The establishment of software can assist researchers in reducing their workload and enhancing data processing efficiency, enabling them to expedite their research progress. The software, along with a detailed user manual, is available at https://github.com/BioCrossCoder/camltree .

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背景：在过去的十年中，生物信息学的持续快速发展使得分子序列比较在系统发生学分析中的应用越来越普遍。然而，多软件和跨平台策略的使用增加了系统发生树估计的复杂性。因此，开发和应用简化的系统发生学分析工具在生物学领域的意义日益重大。特别是对于序列相对较短的基因组来说，缺乏简单而综合的系统发育分析工具：在本研究中，我们介绍了 CamlTree（并列最大似然树），这是一款用户友好型桌面软件，旨在简化病毒和线粒体基因组的系统发生分析，最终促进相关研究。CamlTree 提供的工作流程包括基因连接（或聚合）、序列比对、比对优化以及使用最大似然法（ML）和贝叶斯推断法（BI）估算系统发生树。CamlTree 由 TypeScript 编写，使用 Electron 框架开发。它主要提供基于 React 框架的用户友好界面：CamlTree软件已发布用于Windows操作系统。它集成了几种流行的分析工具，优化并简化了估算多基因系统发生树的过程。该软件的建立可帮助研究人员减少工作量，提高数据处理效率，从而加快研究进度。该软件以及详细的用户手册可在 https://github.com/BioCrossCoder/camltree 上获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

BMC Bioinformatics 生物-生化研究方法

CiteScore

5.70

自引率

3.30%

发文量

506

审稿时长

4.3 months

期刊介绍： BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.