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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Visualization of multiple alignments, phylogenies and gene family evolution
James B Procter1, Julie Thompson, Ivica Letunic
1University of Dundee, UK. j.procter@dundee.ac.uk
Nature Methods
|March 3, 2010
Summary
This review covers software for visualizing sequence alignments and evolutionary trees, aiding gene family studies. It highlights tools ranging from basic viewers to advanced systems, discussing challenges from big data.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence alignment and phylogenetic tree visualization are critical for understanding gene family function and evolution.
- A variety of software tools exist, offering diverse functionalities for researchers.
Purpose of the Study:
- To review and describe key features of stand-alone and web-based software for sequence alignment and tree visualization.
- To aid life scientists in selecting appropriate tools for gene family investigation.
Main Methods:
- Literature review and comparative analysis of selected bioinformatics software.
- Categorization of tools based on features, from simple viewers to complex analysis systems.
Main Results:
- Identified a range of software with varying capabilities for sequence data visualization and analysis.
- Highlighted the utility of these tools in exploring gene family evolution and function.
Conclusions:
- Current visualization tools face challenges due to the exponential increase in next-generation sequencing data.
- The growing complexity of bioinformatics data sources necessitates adaptive and advanced visualization solutions.
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