Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.

[2] Each program is controlled through a menu, which asks users which options they want to set, and allows them to start the computation.

All printable ASCII/ISO characters are allowed names, except for parentheses ("(" and ")"), square brackets ("[" and "]"), colon (":"), semicolon (";") and comma (",").

Relaxed phylip format (sequential): The primary difference in relaxed phylip format is the absence of the 10 character limit and the removal of the need to blank fill names to reach that length (although filling names to start the character matrix at the same position can improve readability for user).

Note that this matrix is symmetric and the diagonal has values of 0 (since the distance between a taxon and itself is zero by definition).