GENETIC SIMILARITIES

 The program was originally designed for comparing sequence of different strains of parasites. Input file is named matrix.txt - it is a text file, every row represents one strain, every row contains only names of bases (A,C,T,G and R,Y,K,M,S,W ) without spaces. The program then computes similarity index for selected bases of every strain combinations (number of the same bases in every pair of bases of compared strains is counted and divided by total number of bases). Output file contained matrix of similarities, matrix of distances (1-similarity), sequence of strains building up the minimum spanning tree and lengths of MST branches. But due the fact that produced distance matrix is based only on similarity index and its Euclideanarity is not sure, it would be better to recompute it using principal coordinate analysis or nonmetric multidimensional scaling and subsequent analysis like minimum spanning tree or cluster analysis perform on such recomputed matrix.

MINIMAL SPANNING TREE

 Minimal Spanning Tree is the smallest sum of n-1 segments that conect n points (Prim, 1957).MST could be computed as a indicator of relative position of points (for example species, strains etc.) in m - dimensional space. MST is computed from matrix of distances between points. For examples of use see Moulton, 1987; Lockwood, 1993; Ricklefs 1980.

Input file is matrix.txt - matrix of distances between points, text file with tabulators as separators.
Output file is log.txt - contains mean and SD of MST, end points of segments, other possible segments ordered by their length and alternative links for ending points of tree.

PRIM RC (1957). Shortest connection networks and some generalizations. Bell System Tech. J. 36: 1389-1401.
LOCKWOOD JL, MOULTON MP, ANDERSON SK (1993). Morphological assortment and the assembly of communities of introduced passeriforms on oceanic islands: Tahiti versus Oahu. The American Naturalist, Vol. 141, No. 3
MOULTON MP and PIMM SL (1987). Morphological assortment in introduced Hawaiian passerines. Evolutionary ecology, 1, 113-124.
RICKLEFS RE and TRAVIS J (1980). A morphlogical approach to the study of avian community organization. The Auk 97: 321-338.

MINIMAL SPANNING TREE SIMULATION

 Minimal Spanning Tree is the smallest sum of n-1 segments that conect n points (Prim, 1957).MST could be computed as a indicator of relative position of points (for example species, strains etc.) in m - dimensional space. MST is computed from matrix of distances between points. For examples of use see Moulton, 1987; Lockwood, 1993; Ricklefs 1980. This program was originally designed for comparing MST of real community with distribution of MSTs of simulated communities. The program builds up 10 000 simulated communities for given number of species (3-14, but it could be easily changed) and computes average segment length and SD of segments of their MSTs from square matrix of distances between species.

PRIM RC (1957). Shortest connection networks and some generalizations. Bell System Tech. J. 36: 1389-1401.
LOCKWOOD JL, MOULTON MP, ANDERSON SK (1993). Morphological assortment and the assembly of communities of introduced passeriforms on oceanic islands: Tahiti versus Oahu. The American Naturalist, Vol. 141, No. 3
MOULTON MP and PIMM SL (1987). Morphological assortment in introduced Hawaiian passerines. Evolutionary ecology, 1, 113-124.
RICKLEFS RE and TRAVIS J (1980). A morphlogical approach to the study of avian community organization. The Auk 97: 321-338.