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INTERALIGN download page

INTERALIGN is a dedicated user friendly alignment editor including a view of secondary structures and a synchronized display of quality carbon alpha traces of corresponding protein structures. Profile alignment using clustalw is implemented to improve the alignment of a sequence of unknown structure with the structurally optimised alignment as compared to a standard multiple sequence alignment. A tree-based ordering helps in identifying the structure closest to a given sequence.

More information is available on the following Help page .

Feb 4th, 2005 : updated information can be found here

Licence
This software is placed under the CeCILL free software licensing agreement: please be sure to read the CeCILL pdf in this directory
Licence.CeCILL-V1.US.pdf or
Licence.CeCILL-V1.pdf in french
before downloading because

Article 3.1 of the CeCILL licence states that:
"The licensee shall be deemed as having accepted the terms and conditions of this Agreement by the occurence of the first of the following events:
-(i) loading the Software by any or all means, notably, by downloading from a remote server, or by loading from a physical medium;

Download

INTERALIGN linux package (27.7MB)
INTERALIGN windows package (20.7MB)
INTERALIGN source files (214kB)

Installation

Under windows
make sure to unzip the interalign_windows_opengl.zip package in a directory without spaces. You can then double click on one of the .bat files in the base directory in windows' File explorer (run_interalign_with_example.bat for instance).
More precisely:
- double click on run_interalign.bat to open the interface without opening an alignment file
- double click on run_interalign_with_example.bat to open the interface with the sample alignment file included in the package in the example subdirectory
- Open easily alignment files with interalign: a nice way to do this is to create a shortcut for run_interalign.bat in your SendTo directory (drive:\Documents and Setting\profile_name\SendTo for win2k or winXP or drive:\windows_dir\SendTo for win98, winME...)then right click on an aln file and choose "Send to" and select the newly created shortcut...

Under Linux
(tested on Redhat 9.0 only) just untar the package in a directory of your choice ( for example tar xfz interalign_linux.tar.gz in the chosen directory) then change to interalign_linux in a shell console and run one of the 2 script files ( open_interalign_with_example for instance )
More precisely:
- type script_interalign in the current directory to run interalign without opening an alignment file
- type open_interalign_with_example in the current directory to open the interface with the sample alignment file included in the package in the example subdirectory
- You pass any absolute aln path name as an argument for script_interalign to open directly your own alignment

After uncompressing the package, you can adapt the paths in config.ini in the interalign subdirectory:
WORKING_DIR=default directory used for opening a file in the File Dialog Window
PDB_DIR=location where local pdb files can be found = might be divided (i.e. bc subdir for abcd.pdb) or not
TEMP_DIR=temporary files directory

Very long paths might cause problems...

Java2 and java3d JRE are installed along with binaries of stride, psipred and clustalw in subdirectories, so everything should be up and running...

You can email me in case of problem...

Version
January 2005 (1.0)

Author

Additional known issues compared to Help page, as of february 4th, 2005:

- sequences names:

• a tentative ncbi style sequence names parser becomes active when a sequence name starts with "gi", trying to access to the sequence name's position. Try avoiding gi starting names if you encounter related crash problems...
• Sequence name length might be mishandled or truncated if longer than 14 characters

- PDB files sequences: sequences extracted from PDB files through "Open PDB file" or "Get sequence and pdb file from PDB ID" do not include "X" residues for non standard amino acids