NONCODE1.exe (a self extracting .zip file) By Eric L. Cabot ecec@midway.uchicago.edu ============================================================================ This program is released to the public domain. The program maybe freely copied and distributed. NONCODE is a Turbo Pascal program that will read an ESEE save file containing nucleic acid sequences and produce a distance matrix using the Kimura 2-parameter model. The main output file contains pairwise analyses for all of the sequences. For each pair a report is generated that consists of # gaps, # transitions, # tranvsersions and estimates of the Kimura parameters A, B and K, and their standard errors. If a gap is found at a position in either of a pair of sequences that position is discluded from the calculation of the parameters. (A modification NOT implemented is this version is the exclusion of the gapped position for all other pairwise coordinates). The source code is provided and heavily commented so that users can easily adapt NONCODE to other platforms or to use data files in other formats. A small program called READGCG is also included as a model to demonstrate how to read "foreign" formats into the internal ESEE record structrue. It is a simple matter to graft the file reading section of READGCG into NONCODE to read files that are in GCG format. ============================================================================= ACKNOWLEDGMENT Thanks to Dr. Chung-I Wu who provided the VMS-Fortran program, also called NONCODE, upon which this program is quite literally based. ============================================================================= Contents of this package NONCODE.exe......for MS-DOS systems NONCODE.pas......Turbo Pascal version 4.0-6.0 READGCG.pas......Demo program showing how to get GCG files into the ESEE internal record structure Test.sav.........Sample Save file Test.out.........Sample of NONCODE outuput TEST.mat.........Sample matrix file TEST.nj..........Sample matrix file Seq-1.gcg........Sample GCG file used to make TEST.sav Seq-2.gcg........Sample GCG file used to make TEST.sav Seq-3.gcg........Sample GCG file used to make TEST.sav READ.ME..........YES, you are reading part of it now!