DISTANCES
Convert multiple alignment data to distance matrix

DISTANCES is a FORTRAN90 program which 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.

Languages:

DISTANCES is available in a FORTRAN90 version.

Related Data and Programs:

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

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

SPACER_DATA_CONVERT, a 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.sh, commands to compile and load the source code;

Examples and Tests:

• distances_input.txt, an input file;
• distances.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.