NEXUS: an extensible file format for systematic information.

@article{Maddison1997NEXUSAE,
  title={NEXUS: an extensible file format for systematic information.},
  author={David R. Maddison and David L. Swofford and Wayne P. Maddison},
  journal={Systematic biology},
  year={1997},
  volume={46 4},
  pages={
          590-621
        }
}
NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing… Expand

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References

SHOWING 1-10 OF 14 REFERENCES
MINIMUM MUTATION FITS TO A GIVEN TREE
SUMMARY A number of objects, such as species, lie at the ends of a known evolutionary tree. A variable taking a finite number of possible values is specified on this set of objects. How can theExpand
Methods for Computing Wagner Trees
Abstract Farris, J. S. (Biol. Sci., State Univ., Stony Brook, N. Y.) 1970. Methods for computing Wagner Trees. Syst. Zool., 19:8342.-The article derives some properties of Wagner Trees and NetworksExpand
Macclade: Analysis of Phylogeny and Character Evolution/Version 3
TLDR
Part I Introducing MacClade: introduction - a tutorial overview of MacClades and an introduction to phylogeny reconstructing character evolution using parsimony stratigraphic parsimony. Expand
Split decomposition: a new and useful approach to phylogenetic analysis of distance data.
TLDR
This work proposes to use a new technique called split decomposition, which accurately dissects the given dissimilarity measure as a sum of elementary "split" metrics plus a (small) residue. Expand
COMPONENT, version 2.0. The Natural History Museum, London
  • SWOFFORD, D. L
  • 1993
Genetic Data Analysis : Software for the analysis of discrete genetic data
  • 1996
Genetic Data Analysis: software for the analysis
  • 1996
TreeBASE
  • A Database of Phylogenetic Knowledge. At the World Wide Web address http://herbaria.harvard.edu/treebase/.
  • 1996
TreeBASE . A database of phylogenetic knowledge
  • Mol . Phylogenet . Evol .
  • 1996
PHYLIP (Phylogeny Inference Package) version 3.5c
  • Distributed by the author. Department of Genetics,
  • 1993
...
1
2
...