DISTANCES
Convert multiple alignment data to distance matrix

DISTANCES is a FORTRAN90 program that reads a multiple alignment file in PIR or FASTA format, computes the distance matrix determined by the alignment, and writes that matrix to a file.

Related Data and Programs:

DISTANCES is also available in a FORTRAN77 version.

READ_ALIGN is an executable FORTRAN90 program which can reformat an alignment file so that it can be examined by DISTANCES.

SPACER is an executable FORTRAN90 program which can read the distance matrix created by DISTANCES and perform a principal component analysis.

SPACER_DATA_CONVERT is an executable FORTRAN90 program which can read a multiple sequence alignment file and write out the relevant information into a file in PIR format.

Author:

Des Higgins,
EMBL Data Library

Source Code:

• distances.f90, the source code;
• distances.csh, commands to compile and load the source code;

Examples and Tests:

• distances_input.txt, an input file;
• distances_output.txt, the output file.
• alignment.txt, a multiple alignment file to be read by DISTANCES;
• alignment.dist, the distance matrix created by DISTANCES;

List of Routines:

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

You can go up one level to the FORTRAN90 source codes.