**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).

**MOVE**.
Interactive construction of phylogenies from discrete character
data with two states (0 and 1). Evaluates parsimony and compatibility
criteria for those phylogenies and displays reconstructed states throughout
the tree. This can be used to find parsimony or compatibility estimates by
hand.

**PENNY**.
Finds all most parsimonious phylogenies for discrete-character
data with two states, for the Wagner, Camin-Sokal, and mixed parsimony
criteria using the branch-and-bound method of exact search. May be
impractical (depending on the data) for more than 10-11 species.

**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.

**DOLMOVE**.
Interactive construction of phylogenies from discrete
character data with two states (0 and 1) using the Dollo or polymorphism
parsimony criteria. Evaluates parsimony and compatibility criteria for
those phylogenies and displays reconstructed states throughout the tree.
This can be used to find parsimony or compatibility estimates by hand.

**DOLPENNY**.
Finds all most parsimonious phylogenies for
discrete-character data with two states, for the Dollo or polymorphism
parsimony criteria using the branch-and-bound method of exact search. May
be impractical (depending on the data) for more than 10-11 species.

**CLIQUE**.
Finds the largest clique of mutually compatible characters, and
the phylogeny which they recommend, for discrete character data with two
states. The largest clique (or all cliques within a given size range of
the largest one) are found by a very fast branch and bound search method.
The method does not allow for missing data. For such cases the `T`
(Threshold) option of PARS or MIX may be a useful alternative.
Compatibility methods are particular useful when some characters are of
poor quality and the rest of good quality, but when it is not known in
advance which ones are which.

**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.

**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.

**CONSENSE**.
Computes consensus trees by the majority-rule consensus tree
method, which also allows one to easily find the strict consensus tree.
Is not able to compute the Adams consensus tree. Trees are input in a tree
file in standard nested-parenthesis notation, which is produced by many of
the tree estimation programs in the package. This program can be used as
the final step in doing bootstrap analyses for many of the methods in the
package.

... to the PHYLIP home page