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
- Click NWalign.java.tar.bz2 to download a Java version of
the NW-align code.
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