Noisy: Identification of problematic columns in multiple sequence alignments
2008
Identifying Noisy Columns in Sequence Alignments
publication
Evidence: moderate
Author Information
Author(s): Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J Prohaska, Peter F Stadler
Hypothesis
Can we improve phylogenetic reconstruction by identifying and removing noisy sites in multiple sequence alignments?
Conclusion
The method presented improves phylogenetic reconstruction by removing uninformative homoplastic sites from alignments.
Supporting Evidence
- The software 'noisy' effectively identifies and removes problematic alignment columns.
- Removal of noisy sites leads to more stable phylogenetic trees.
- The method is based on assessing the distribution of character states along a cyclic ordering of taxa.
Takeaway
This study shows how to find and remove bad parts of DNA sequences to make better family trees of living things.
Methodology
The method assesses character state distributions along a cyclic ordering of taxa to identify uninformative sites.
Limitations
The method may not be effective for very small datasets with fewer than 10 taxa.
Digital Object Identifier (DOI)
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