DISTANCES - Convert multiple alignment to distances

DISTANCES is a program that reads a multiple alignment file in PIR or FASTA format, computes a distance matrix determined by the alignmen, and writes that matrix to a file. In some cases, the READ_ALIGN program can be used to reformat an alignment file for use with DISTANCES.

Once the distance matrix is created, it may be used in a principal coordinate analysis, such as that computed by SPACER.

Author:

Des Higgins,
EMBL Data Library,
April 1992.

Files you may copy include:

• distances.f90, the source code;
• alignment.txt, a multiple alignment file;
• alignment.dist, the distance matrix file;

The list of routines includes:

• DISTANCES reads a multiple alignment file and outputs a distance matrix.
• DIST_MAT_WRITE writes the distance matrix to a file.
• SET_AAMAT sets up the amino acid distance matrix.
• SET_AASCORE updates a match matrix with a group of matching data.
• TOSS_GAPS obliterates information in a position where any sequence has a gap.
• DIST_MAT_SET calculates a matrix of distances between pairs of sequences.
• READ_SEQUENCE reads a FASTA or PIR format multiple alignment file.

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