DISTANCES
Convert multiple alignment data to distance matrix

DISTANCES is a FORTRAN77 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.

Related Data and Programs:

DISTANCES is also available in a FORTRAN90 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.f, 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:

• MAIN is the main program for DISTANCES.
• SETAAMAT
• SETAASCORE
• TOSSGAPS
• CHFEXT changes the extension of a filename.
• DISTMAT calculates a similarity matrix between pairs os sequences.
• READSEQS reads a FASTA or PIR format multiple aligment file.
• GETSTR prompts for a string input.
• GETINT prompts for an integer input.

You can go up one level to the FORTRAN77 source codes.