NW-align is simple and robust alignment program for
protein sequence-to-sequence alignments based on the standard
Needleman-Wunsch dynamic programming algorithm. The
mutation matrix is from BLOSUM62 with
gap openning penalty=-11 and gap extension penalty=-1.
The source code of this program can be downloaded at
the bottom of this page, which can be easily modified
for different purposes.
A Java code using the standard Smith-Waterman
algorithm for local sequence alignment was recently added
in the page as well.
Click NWalign to download the executable program
for Linux system. Simply running the program itself will give you a brief
instruction of how to use it
(In case that you are using a 32 bit computer and you get warning
message of "bash: ./NWalign: cannot execute binary file", you need to
download the source code and compile the program on your machine. See below).
Click NWalign.f to download the source code of NW-align
coded in Fortran77. You can compile the program in your computer by
>gfortran -static -O3 -ffast-math -lm -o NWalign NWalign.f
>g77 -static -O3 -lm -o NWalign NWalign.f
to download a Java version of
the SW-align code, which was designed to align two protein sequences using the standard
Different from NW-align which is for global sequence alignment, SW algorithm is
designed for optimal local sequence alignments.
click BLOSUM62.txt to download the BLOSUM62
Substitution Matrix that is used in the NW-align program.
Y. Zhang, http://zhanglab.ccmb.med.umich.edu/NW-align