**FITCH**.
Estimates phylogenies from distance matrix data under the
"additive tree model" according to which the distances are expected to
equal the sums of branch lengths between the species. Uses the
Fitch-Margoliash criterion and some related least squares criteria, or
the Minimum Evolution distance matrix method. Does
not assume an evolutionary clock. This program will be useful with
distances computed from molecular sequences, restriction sites or fragments
distances, with DNA hybridization measurements, and with genetic distances
computed from gene frequencies.

**KITSCH**.
Estimates phylogenies from distance matrix data under the
"ultrametric" model which is the same as the additive tree model except
that an evolutionary clock is assumed. The Fitch-Margoliash criterion and
other least squares criteria, or the Minimum Evolution criterion are
possible. This program will be useful with
distances computed from molecular sequences, restriction sites or
fragments distances, with distances from DNA hybridization measurements,
and with genetic distances computed from gene frequencies.

**NEIGHBOR**.
An implementation by Mary Kuhner and John Yamato of Saitou and
Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage
clustering) method. Neighbor Joining is a distance matrix method producing
an unrooted tree without the assumption of a clock. UPGMA does assume a
clock. The branch lengths are not optimized by the least squares criterion
but the methods are very fast and thus can handle much larger data sets.

**DNADIST**.
Computes four different distances between species from nucleic acid
sequences. The distances can then be used in the distance matrix programs.
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 in a prespecified way, and also
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 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.

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