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Tools for distance-based phylogenetic trees.
General data analysis tools.

Software is designed for UNIX, it is written in C++ and bash scripts.
Running an executable without parameters prints a short instruction.
Running a C++ executable with the parameter -help prints an instruction on parameters.

Definitions

An object is something (gene, genome) that evolves making up an evolution tree.
The interior nodes if this tree are extinct objects, whereas the leaves of this tree are extant objects.
The dissimilarity d between two objects is the length of the path between the two tree nodes plus a random noise.

d(x,y) >= 0
d(x,y) = d(y,x)
if x = y then d(x,y) = 0

A distance tree of a set of objects is an estimation of their evolution tree where each object is a leaf and the distances between tree leaves approximate the dissimilarities between the objects.
A reservoir of objects is a collection of objects (directory, database table) which are used for incremental tree building.
Each object should have a name - a sequence of alpha-numeric characters or '_' symbols.
A list of objects is a file where each line is an object name.