**DNADIST**. Computes
four different distances between species from nucleic acid
sequences. The distances can then be used in the distance matrix programs.
(See the Distance Matrix programs pages for information on them).
The distances are the Jukes-Cantor formula, one based on Kimura's 2-
parameter method, the F84 model used in DNAML, and the LogDet distance.
The distances can also be corrected for gamma-distributed and
gamma-plus-invariant-sites-distributed rates of change in different sites.
Rates of evolution can vary among sites either in a prespecified way, or
according to a Hidden Markov model. The program can also make a table of
percentage similarity among sequences.

**PROTDIST**.
Computes a distance measure for protein sequences, using
maximum likelihood estimates based on the Dayhoff PAM matrix,
the JTT matrix model, the PBM model, Kimura's 1983 approximation to these,
or a model based on the genetic code plus a constraint on changing to a
different category of amino acid. The distances can also be corrected for
gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a
prespecified way, and also according to a Hidden Markov model. The program
can also make a table of percentage similarity among sequences. The
distances can then be used in the distance matrix programs.

**GENDIST**. Computes one of three different genetic distance formulas from gene
frequency data. The formulas are Nei's genetic distance, the Cavalli-
Sforza chord measure, and the genetic distance of Reynolds et. al. The
former is appropriate for data in which new mutations occur in an infinite
isoalleles neutral mutation model, the latter two for a model without
mutation and with pure genetic drift. The distances are written to a file
in a format appropriate for input to the distance matrix programs.

**RESTDIST**.
Distances calculated from restriction sites data or
restriction fragments data. The restriction sites option is the one to
use to also make distances for RAPDs or AFLPs. The distances can then
be used with the distance matrix programs

**SEQBOOT**.
Reads in a data set, and produces multiple data sets from
it by bootstrap resampling. Since most programs in the current version of
the package allow processing of multiple data sets, this can be used
together with the consensus tree program CONSENSE to do bootstrap (or
delete-half-jackknife) analyses with most of the methods in this package.
This program also allows the Archie/Faith technique of permutation of
species within characters. It can also rewrite a data set to convert
it from between the PHYLIP Interleaved and Sequential forms, and into
a preliminary version of a new XML sequence alignment format
which is under development and which is described in the
SEQBOOT documentation web page.

**FACTOR**.
Takes discrete multistate data with character state trees and
produces the corresponding data set with two states (0 and 1). Written by
Christopher Meacham. This program was formerly used to accomodate
multistate characters in MIX, but this is less necessary now that PARS is
available.

... to the PHYLIP home page