Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
Abstract
A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: "once a gap, always a gap." The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.
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Progressive Cactus incorporates a progressive alignment strategy that changes the runtime to scale linearly with the number of genomes.
“we present fundamental changes to the Cactus process that incorporate a progressive alignment strategy15, which changes the runtime of the alignment to scale linearly with the number of genomes.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [15]
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- Authors
- Feng, D.-F., & Doolittle, R. F.
- Affiliations
- University of California San Diego (US)
- Venue
- Journal of Molecular Evolution
- Published
- 1987-08
- Volume
- 25
- Issue
- 4
- Pages
- 351-360
- ISSN
- 0022-2844 (ISSN-L)
- 1432-1432
- OpenAlex
- W1969153299
- Cited by
- 1,883
- References
- 1
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 25 · 2023: 20 · 2022: 27 · 2021: 33 · 2020: 23 · 2019: 27 · 2018: 40 · 2017: 37 · 2016: 28 · 2015: 41 · 2014: 34 · 2013: 42 · 2012: 28
- FWCI
- 17.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Molecular Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM 34434)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- multiple sequence alignment, phylogenetic tree construction, Needleman-Wunsch algorithm, protein sequences, superoxide dismutase, globin, gap penalties, sequence divergence
- MeSH terms
- Algorithms, Amino Acid Sequence, Animals, Biological Evolution, Hemoglobins, Humans, Methods, Phylogeny, Protein-Tyrosine Kinases, Proteins, Superoxide Dismutase
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