The RESTSITE v.1.2 Software Package

RESTSITE 1994 by Joyce C. Miller.

RESTSITE is a suite of computer programs that I wrote while working as a postdoctoral fellow with Dr. Masatoshi Nei. The programs process text files of restriction site or restriction fragment data for evolutionary analysis. The programs are written in Microsoft C, for DOS. There is no Mac version, sorry. If someone wants to port these over to Mac or UNIX systems, or include them in another software package, please contact me.

Descriptions of the files:

  • READTEXT - reads ASCII text files where each line contains data from one individual cut with one enzyme and probed with one probe (one "lane"). A binary data file is produced.
  • WRITETXT - reads binary data files and converts them back into ASCII. This aids portability to other machines.
  • RESTSITE - reads binary data files, groups the data into OTUs specified by the user, extracts the sites/fragments in common, and calculates the distance between the OTUs. Also produces distance matrices.
  • REPORT - generates a listing of the data found within each OTU, broken down by enzyme and probe.
  • CALCD - a stand-alone program that computes d-hat via equations 5.53-5.55 of Nei (1987), when given the fragments found in OTU X, Y, and in common.
  • REMFILE - temporarily removes an OTU from the study.
  • COMBINE - temporarily combines two OTUs into one.
  • REMDATA - temporarily removes the data found in one OTU from another OTU (useful in finding species-specific sites/fragments).
  • 01_TO_RS - converts 0/1 data matrices to RESTSITE format.
  • RS_TO_01 - converts RESTSITE data to 0/1 matrices.
  • NJTREE - constructs Neighbor-Joining trees from distance matrices.
  • UPGMA - constructs UPGMA trees from distance matrices.

    If you want to dowload the package, I recommend that you take not only the programs, but also the documentation and the sample data. The documentation explains how to prepare your data and how to use the programs properly, so that you don't use the wrong types of analyses on the wrong types of molecular data. The sample data files are useful as a "check" to be sure that the programs are running correctly on your computer. If you get the same answers as in the documentation, you're fine.

    The source code is also available, but please don't incorporate these programs into any other programs or software packages without talking to me first. I did spend a year of my life writing them and I do own them, even though I make them freely available to the scientific community.

    References:

  • Nei, M., and J.C. Miller (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125:873-879.
  • Miller, Joyce C. (1991) RESTSITE: A phylogenetic program that sorts raw restriction data. Journal of Heredity 82:262-263.

    If you have any questions or problems, you can e-mail me at

    jmiller@genome.wi.mit.edu

    Last updated 5 June, 1996.

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