**PROTPARS**. Estimates phylogenies from protein sequences (input using the
standard one-letter code for amino acids) using the parsimony method, in
a variant which counts only those nucleotide changes that change the amino
acid, on the assumption that silent changes are more easily accomplished.

**DNAPARS**.
Estimates phylogenies by the parsimony method using nucleic acid
sequences. Allows use the full IUB ambiguity codes, and estimates
ancestral nucleotide states. Gaps treated as a fifth nucleotide state.
It can also fo transversion parsimony. Can cope with multifurcations,
reconstruct ancestral states, use 0/1 character weights, and infer branch
lengths.

**DNACOMP**.
Estimates phylogenies from nucleic acid sequence data using
the compatibility criterion, which searches for the largest number of sites
which could have all states (nucleotides) uniquely evolved on the same
tree. Compatibility is particularly appropriate when sites vary greatly in
their rates of evolution, but we do not know in advance which are the less
reliable ones.

**DNAML**.
Estimates phylogenies from nucleotide sequences by maximum
likelihood. The model employed allows for unequal expected frequencies of
the four nucleotides, for unequal rates of transitions and transversions,
and for different (prespecified) rates of change in different categories of
sites, and also use of a Hidden Markov model of rates, with
the program inferring which sites have which rates. This also
allows gamma-distribution and gamma-plus-invariant sites distributions of
rates across sites.

**DNAMLK**. Same as DNAML but assumes a molecular clock. The use of the
two programs together permits a likelihood ratio test of the
molecular clock hypothesis to be made.

**PROML**.
Estimates phylogenies from protein amino acid sequences by maximum
likelihood. The PAM, JTT, or PMB models can be employed, and also use
of a Hidden Markov model of rates, with the program inferring which sites
have which rates. This also allows gamma-distribution and
gamma-plus-invariant sites distributions of rates across sites.
It also allows different rates of change at known sites.

**PROMLK**.
Same as PROML but assumes a molecular clock. The use of the
two programs together permits a likelihood ratio test of the
molecular clock hypothesis to be made.

**RESTML**. Estimation of phylogenies by maximum likelihood using restriction
sites data (not restriction fragments but presence/absence of individual
sites). It employs the Jukes-Cantor symmetrical model of nucleotide
change, which does not allow for differences of rate between transitions
and transversions. This program is VERY slow.

**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.

**CONTML**.
Estimates phylogenies from gene frequency data by maximum
likelihood under a model in which all divergence is due to genetic drift in
the absence of new mutations. Does not assume a molecular clock. An
alternative method of analyzing this data is to compute Nei's genetic
distance and use one of the distance matrix programs.
This program can also do maximum likelihood analysis of continuous
characters that evolve by a Brownian Motion model, but it assumes that
the characters evolve at equal rates and in an uncorrelated fashion, so
that it does not take into account the usual correlations of characters.

**PARS**.
Multistate discrete-characters parsimony method. Up to 8 states
(as well as "`?`") are allowed. Cannot do Camin-Sokal or Dollo Parsimony.
Can cope with multifurcations, reconstruct ancestral states, use character
weights, and infer branch lengths.

**MIX**.
Estimates phylogenies by some parsimony methods for discrete
character data with two states (0 and 1). Allows use of the
Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary
mixtures of these. Also reconstructs ancestral states and allows weighting
of characters (does not infer branch lengths).

**DOLLOP**.
Estimates phylogenies by the Dollo or polymorphism parsimony
criteria for discrete character data with two states (0 and 1). Also
reconstructs ancestral states and allows weighting of characters. Dollo
parsimony is particularly appropriate for restriction sites data; with
ancestor states specified as unknown it may be appropriate for restriction
fragments data.

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