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Sample NEXUS files


Input files for PAUP* are standard text files containing commands and/or data, which adhere to the NEXUS file format. PAUP* 4.0 is also capable of translating other file formates, such as, Phylip, Hennig86, text, GCG, Mega, PIR, and FreqPars to the NEXUS format. NEXUS files may be viewed and edited in any text editor or in packages like MacClade (Mac) or NDE (PC). The NEXUS format was designed by David Maddison, Wayne Maddison, and David Swofford to facilitate the interchange of input files between programs used in phylogeny and classification. For a more complete explanation of the NEXUS format see:

Maddison, D. R., Swofford, D. L., Maddison, W. P. 1997. NEXUS: An extensible file format for systematic information. Systematic Biology 46(4):590-621.

Sample NEXUS files:

  • angiosperms.nex [Young, D. A. 1981. Are the angiosperm primitively vesselless?
    Systematic Botany. 6:313-330.]
  • avian-ovomucoids.nex [Laskowski, M., Jr., and W.M. Fitch. 1989. Evolution of avian ovomucoids and of birds. Pp. 371-387 in B. Fernholm, K. Bremer, and H. Jrnvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam.]
  • primate-mtDNA-interleaved.nex [Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.]
  • primate-mtDNA.nex [Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.]

Sample Analyses:

  • ML_analysis.nex -- This file contains a simulated DNA data set followed by a PAUP block with instructions to conduct a likelihood analysis.
  • MP_analysis.nex -- This file contains two simulated DNA data sets, an assumption block, a sets block, and a paup block. The paup block demonstrates how to do a heuristic search under the parsimony criteria and a partition homogeneity test.
  • PROTPARS-example.nex [This example demonstrates the use of PAUP to perform an analysis equivalent to Felsenstein's PROTPARS program from the PHYLIP package. Stepmatrices are constructed which specify the minimum number of amino acid replacements required to convert one amino acid to another. (Silent nucleotide substitutions are "free".)]
  • blosum62.nex [A stepmatrix constructed from Blosum62 amino acid transition matrix of Henikoff & Henikoff (1992, PNAS USA 89:10915-10919). Because there are negative values in the original Blosum62 matrix, the most negative value was set equal to 0 and all other values were increased correspondingly. Scores for transitions to and from gaps were not defined in the original matrix. They have been set equal to the most costly transition (15) defined in the matrix. These modifications were made by R. K. Kuzoff]
  • pam250.nex [A stepmatrix constructed from PAM250 amino acid transition matrix of Dayhoff et al. (1978, In Atlas of Protein Sequence Structure, ed. M. O. Dayhoff, Washington, DC: National Biomedical Research Foundation). Because there are negative values in the original PAM250 matrix, the most negative value was set equal to 0 and all other values were increased correspondingly. Scores for transitions to and from gaps were not defined in the original matrix. They have been set equal to the most costly transition (25) defined in the matrix. These modifications were made by R. K. Kuzoff]

Sample file formats that PAUP will import:

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