Analyzing large data sets in reasonable times: solutions for composite optima
Open accessAbstract
New methods for parsimony analysis of large data sets are presented. The new methods are sectorial searches, tree‐drifting, and tree‐fusing. For Chase et al. 's 500‐taxon data set these methods (on a 266‐MHz Pentium II) find a shortest tree in less than 10 min (i.e., over 15,000 times faster than PAUP and 1000 times faster than PAUP*). Making a complete parsimony analysis requires hitting minimum length several times independently, but not necessarily all “islands” for Chase et al. 's data set, this can be done in 4 to 6 h. The new methods also perform well in other cases analyzed (which range from 170 to 854 taxa).
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A common problem in palaeontological studies is the extremely large numbers of equally parsimonious trees (due to missing entries), but the consensus stabilization procedure can produce an accurate consensus without finding all equally possible most parsimonious trees.
“A common problem in palaeontological studies is the extremely large numbers of equally parsimonious trees (due to missing entries), but the consensus stabilization procedure can produce an accurate consensus without finding all equally possible most parsimonious trees (thus greatly saving in computational effort [100]).”
From Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds (2020) · cites this paper as [100]
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“Goloboff PA. 1999.”
- Authors
- Goloboff, P. A.
- Affiliations
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Corresponding author
- Goloboff, Pablo A.
- ORCID
- Goloboff, Pablo A.
- Venue
- Cladistics
- Publisher
- Wiley
- Published
- 1999-12
- Volume
- 15
- Issue
- 4
- Pages
- 415-428
- ISSN
- 0748-3007 (ISSN-L)
- 1096-0031
- OpenAlex
- W2106179083
- Cited by
- 1,039
- References
- 25
- Citations by year
- 2026: 13 · 2025: 23 · 2024: 35 · 2023: 30 · 2022: 32 · 2021: 48 · 2020: 53 · 2019: 33 · 2018: 38 · 2017: 41 · 2016: 55 · 2015: 32 · 2014: 76 · 2013: 66 · 2012: 55
- FWCI
- 2.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cladistics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Washington
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- parsimony analysis, large data sets, phylogenetic tree search, computational efficiency
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