Biology Reference
In-Depth Information
3 GramAlign Usage
gramalign.php
for both source code download and a web-based
alignment server.
GRAMALIGN
is written in ANSI-C, and so should build without error
on any platform with an ANSI-C compiler. Use the following
commands to build the program.
3.1
Install
cd src
make clean
make
At this point, the console-based executable
GramAlign
(on
linux/MacOSX) or
GramAlign.exe
(on Windows) will reside in
the src directory as well. Copy the executable to anywhere in your
path.
To run
GRAMALIGN
from the command-line window, use the follow-
ing command:
3.2 Usage
/path/to/executable/GramAlign [options]
Examples:
The most basic example performs an alignment for the
sequences in the file “input.fasta,” which is located on the user's
desktop. The output is written to a file named “output.txt,” also on
the desktop.
GramAlign -i ~/Desktop/input.fasta -o ~/Desktop/output.txt
An example of applying two additional options creates a dis-
tance matrix for the sequences in the file “input.fasta.” Supplying
the “-C” option tells the program to compute the full distance
matrix, and the program's output is written to “output.txt.” As in
the previous example, the input and output files are accessed on the
desktop based on the provided path.
GramAlign -f 0 -C -i ~/Desktop/input.fasta -o ~/Desktop/
output.txt
3.3 General Options
The most generic options include the following:
Option -h
: Help! Display the command-line options.
Option -q
: Turn on “quiet mode,” which will prevent any inter-
mediate text from being displayed by
GRAMALIGN
. The default is
verbose which will output various progress during the alignment
procedure.
Option -S <value>
: Specify the maximum trace-back matrix size
before temporary paging begins. The largest one-time memory
requirement for
GRAMALIGN
occurs during each pairwise alignment
