PyMood BLAST Output Files for the PyMood Pipeline matrix Files

For every BLAST output, PyMood BLAST parser will create a matrix file with the extension .matrix
An example would be:
worm_vs_fly.blastp.matrix
This file can be opened in any spreadsheet editor. The file contains eight columns, where:

     A. unique identifier for the query gene
     B. unique identifier of the best BLAST hit in the target database, if it is above the cutoff of the 'Expect value'
     C. normalized* expectation values
     D. score (bits)
     E. percentage of identity** between the overlapping regions
     F. number of identical letters in the overlap
     G. length of the overlap
     H. shows 1 if there is a BLAST hit found

     * normalized expectation value reflects the absolute value of the exponent in the expectation value. If the expectation value is 2e-15, the normalized expectation value is 15. For all expectation values better than e-100, like 3e-101, 7e-156, etc., the normalized expectation value 100 is assigned.

     ** if you prefer to use the percentage of identity instead of normalized expectation values for visualization of your BLAST outputs, you will need to switch the columns 3 and 5, so that column 5 becomes the column 3 in the matrix file. The file must be saved as a tab delimited text file with the extension .matrix