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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Kazutaka Katoh1, Daron M Standley

  • 1Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan. kazutaka.katoh@aist.go.jp

Molecular Biology and Evolution
|January 19, 2013
PubMed
Summary
This summary is machine-generated.

This update introduces new features to the MAFFT multiple sequence alignment program, enhancing its capabilities for biological sequence analysis. The report details these advancements and discusses strategies to improve alignment accuracy.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment is crucial for understanding evolutionary relationships and functional genomics.
  • The MAFFT program is a widely used tool for efficient and accurate sequence alignment.
  • Previous versions of MAFFT have set benchmarks in speed and accuracy.

Purpose of the Study:

  • To report a major update to the MAFFT multiple sequence alignment software.
  • To introduce and explain new features implemented in the latest MAFFT version.
  • To demonstrate the utility and limitations of these new features through practical examples.

Main Methods:

  • Implementation of new features: unaligned sequence addition, nucleotide direction adjustment, constrained alignment, and parallel processing.
  • Illustrative examples showcasing the application of new features individually and in combination.
  • Analysis of specific cases where MAFFT may produce suboptimal alignments.

Main Results:

  • The updated MAFFT program now supports dynamic addition of unaligned sequences.
  • New options for nucleotide alignment direction and constrained alignment have been introduced.
  • Parallel processing capabilities have been enhanced for faster alignments on multi-core systems.

Conclusions:

  • The latest MAFFT version offers advanced functionalities for complex multiple sequence alignment tasks.
  • Understanding MAFFT's limitations and employing appropriate strategies can help avoid misalignments.
  • Ongoing development aims to further enhance the accuracy and robustness of MAFFT.