Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

MaxAlign: maximizing usable data in an alignment.

Rodrigo Gouveia-Oliveira1, Peter W Sackett, Anders G Pedersen

  • 1Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark. rodrigo@cbs.dtu.dk

BMC Bioinformatics
|August 30, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction.

Virus evolution·2025
Same author

Tracking mucosal innate immune responses to three influenza A virus strains in a highly translational pig model using nasopharyngeal swabs.

Innate immunity·2025
Same author

Expanding known viral diversity in the healthy infant gut.

Nature microbiology·2023
Same author

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira.

Microbiome·2022
Same author

Genome-wide study of early and severe childhood asthma identifies interaction between CDHR3 and GSDMB.

The Journal of allergy and clinical immunology·2022
Same author

FUT2-ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses.

Nature communications·2020
Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
See all related articles

MaxAlign optimizes sequence alignments by removing problematic sequences, improving phylogenetic analysis accuracy. This method helps identify poor-quality sequences and enhances the reliability of evolutionary studies.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Gaps in sequence alignments pose challenges for bioinformatics and phylogenetic studies.
  • Gapped columns are often removed, potentially leading to loss of information.

Purpose of the Study:

  • To introduce and evaluate MaxAlign, a program for optimizing sequence alignments.
  • To assess the impact of MaxAlign on phylogenetic accuracy and sequence quality detection.

Main Methods:

  • MaxAlign identifies optimal subsets of sequences to exclude, maximizing gap-free alignment regions.
  • Phylogenetic accuracy was compared with and without MaxAlign processing and gapped column exclusion.
  • A new tree similarity measure, Normalized Symmetric Similarity (NSS), was introduced.

Related Experiment Videos

Main Results:

  • MaxAlign effectively identifies misaligned or defective sequences without manual review.
  • Excluding gapped columns without MaxAlign processing can reduce phylogenetic accuracy.
  • Sequences removed by MaxAlign are often those associated with lower phylogenetic accuracy.

Conclusions:

  • MaxAlign improves sequence alignment quality for downstream analyses like phylogenetics.
  • It is advisable to use MaxAlign before removing gapped columns in phylogenetic analyses.
  • The MaxAlign tool is available as a web server and a standalone package.