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

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 e...

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Vydáno v:BMC bioinformatics Ročník 26; číslo 1; s. 53 - 14
Hlavní autoři: Sun, Peng, Yang, Yu, Yuan, Mengjie, Tang, Qin
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 14.02.2025
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Algorithms
Alignment
Applications software
Automation
Bayes Theorem
Bayesian analysis
Bioinformatics
Biomedical and Life Sciences
Coalescence
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Data processing
Estimation
Fourier transforms
Genes
Genetic research
Genome, Mitochondrial
Genome, Viral
Genomes
Infrastructure
Integration
JavaScript
Life Sciences
Likelihood Functions
Linux
Maximum likelihood estimates (Statistics)
Microarrays
Mitochondrial DNA
Mitochondrion
Nucleotide sequence
Operating systems
Optimization
Phylogenetic analysis
Phylogenetics
Phylogeny
Sequence Alignment
Software
Statistical inference
Streamlined workflow
User interface
Viral genetics
Virus
Workflow
China
Virus
Mitochondrion
Phylogenetic analysis
Integration
Streamlined workflow
Optimization
ISSN:1471-2105, 1471-2105
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Shrnutí: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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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-025-06034-2