POP

Parameter Optimization Procedure

Developed by Robert C. Edgar.

Citation

Edgar RC., Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics, 2009 Dec 2;10:396.

Improved CLUSTALW

This is the CLUSTALW command-line which gave an 8% improvement on BALIBASE v3.

clustalw -infile=filename -outfile=filename -align -matrix=VTML200 -gapopen=2.0 -gapext=0.1

Here is the VTML200 matrix.

I used version 2.0.9 of CLUSTALW.

Downloads

All files are in "tarball" format, use tar -zxvf filename to extract files.

Linux executable (32-bit)

Linux executable (64-bit)

Windows executable (32-bit)

Source code

Test sets

BLOSUM62 in 1/3-bit units