Download academic (non-commercial) version of Phobos,
Copyright (c) Christoph Mayer 2006-2017:
The download counter of Phobos is approaching 10,000. This is a great success.
Please report any bugs you discover or any problems you have when trying to get the program to work.
If you are using the Linux platform, please tell me if you should experince the problem that on your system non of the binaries work.
I will try to fix this issue.
Content of the downloadable zip-archives:
- GUI (graphical user interface) version(s) of Phobos (usually only for Mac, Linux, Windows)
- CL (command-line) version(s) of Phobos
- Quickstart.txt file with installation and Quick Start instructions
- Known-Phobos-bugs.txt file with known bugs of older and current version of Phobos
- phobos-manual-*.pdf - Phobos manual
- folder with example data sets
I can't find the operating system I am looking for:
Mac, Linux, and Windows executables will be made available for all major versions.
Other operating systems are supported only upon request and only if I manage to find a machine to
build the executable. Please contact me if non of the linux binaries work on your machine.
Primer design and visualisation:
- STAMP-module for Staden pipeline - is known to work with version 3.3.2 of Phobos. Version 3.3.11 is currently being tested.
- Phobos plugin for Geneious. Requires command-line version of Phobos (version 3.3.10 or higher).
See Phobos homepage for details.
Most resent version: 3.3.12 (September 2010, new Linux binaries added September 2017)
What's new in version 3.3.12:
- Fixed a bug, where trailing spaces in sequence names could cause a segmentation fault in the library function that reads the fasta input file.
The last major version was from September 2010 and users might ask: Is Phobos still maintained and supported? Yes. There have been no bug reports
for a long long time. This is good news for all users.
I still intend to improve the main algorithm to make it even faster. But my time is limited and it won't be in the very near future.
For 99.9% of the users speed is no problem anyway.
If you have problems or if, unexpectedly, you discover a bug, please contact me!
Download Phobos
version 3.3.12 for Linux as zip
Download Phobos
version 3.3.12 for Linux as tar.gz
Download Phobos
version 3.3.12 for Mac Os X (Intel/PPC)
Download Phobos
version 3.3.12 for Windows
Version: 3.3.11 (Mai 2010)
What's new in version 3.3.11:
- Fixed a bug, where the repeat positions could be reported wrong, if gaps or
*'s occur in the sequence. This bug did not effect users of the Geneious plugin!
- Fixed a bug in the GUI of Phobos, where the reset
button did not reset the "Treat Ns as missense"
check box.
- New parameters: --maskLower, --convert_gaps_to_Ns and --STAMPrun
On July, 27th the following bug has been reported: Trailing spaces in sequence names can cause a segmentation fault in the library function that reads the fasta input file.
There will soon be an new version fixing this bug. In the meantime please make sure sequence names have no trailing spaces. Sorry for this inconvenience.
A new Version, which corrects this bug will be available before Sept. 15th. If you do not have trailing spaces in sequence names
version 3.3.11 will work fine.
Download Phobos
version 3.3.11 for Linux as zip
Download Phobos
version 3.3.11 for Linux as tar.gz
Download Phobos
version 3.3.11 for Mac Os X (Intel/PPC)
Download Phobos
version 3.3.11 for Windows
Version: 3.3.10 (September 2009)
What's new in version 3.3.10:
- Version 3.3.10 fixes all known issues of version 3.3.2.
- In Version 3.3.10 the default values of several search parameters have changed:
* Default values for the mismatch and gap penalty now are: -5 (used to be -6)
* For two variants of a tandem repeats with the same alignment score Phobos now reports the longer variant. (Used to be the shorter variant.)
With the new default values Phobos is looking for more imperfect repeats. This increases the run-time of Phobos.
The old default behaviour can be obtained with the following command-line parameters: -m -6 -g -6 --preferShorterRepeats
- New output formats: gff - general feature format, one-per-line format, FASTA-format.
- The commercial DNA and protein analysis tool Geneious now provides a plugin to integrate Phobos. This requires the command-line version of Phobos (version 3.3.10 or higher). (Is coming up soon)
Commercial users of Phobos that are using Phobos in Geneious still need to obtain a license for Phobos from the author Christoph Mayer.
- For the Staden package we developed the STAMP module which allows to use Phobos to detect tandem repeats and design flanking primers.
Please see the Phobos web site for details.
Download Phobos version 3.3.10 for Linux as zip
Download Phobos version 3.3.10 for Linux as tar.gz
Download Phobos version 3.3.10 for Mac Os X (Intel/PPC)
Download Phobos version 3.3.10 for Windows
Version 3.3.2: (28 August 2008)
What's new in version 3.3.2:
- Version 3.3.2 fixes all known issues of version 3.2.6.
- GUI now runs on Mac Os X Leopard.
- Version 3.3.2 is significantly faster for small mismatch and indel penalty scores and when searching for longer repeat units.
- The minimum unit length is not restricted to 1 or 2 any more, but can be any length smaller or equal to the maximum unit length.
- New search parameter: "maximum score reduction", which makes Phobos much faster with little loss of accuracy.
- Does not crash any more when reading a bad fasta file, but reports an error.
Remark: the subversions 3.3.2b and 3.3.2c are identical
Download Phobos version 3.3.2b for Linux (Indel and AMD64 versions included)
Download Phobos version 3.3.2b for Mac Os X (Intel)
Download Phobos version 3.3.2b for Mac Os X (PPC)
Download Phobos version 3.3.2c for Solaris 10 (i386 and sparc)
Download Phobos version 3.3.2c for Windows
Deprecated version 3.2.6: (23 January 2008)
Known bugs in Phobos version 3.2.6:
* The GUI version of Phobos 3.2.6 has a bug that can lead to faulty output:
In contrast to the CL-version of Phobos, the GUI allows several successive analyses without
restarting the program. If after the first analysis the mismatch or gap penalty and/or
the minimum or maximum unit size are changed, the output is not correct. Thus, in version 3.2.6 the
GUI should only be used for a single analysis. Before further analyses the program has to be
restarted. The CL version of Phobos is not affected.
* The GUI does not work on Mac OS X Leopard.
Download Phobos version 3.2.6 for Mac Os X (PPC)
Download Phobos version 3.2.6 for Mac Os X (Intel)
Download Phobos version 3.2.6 for Linux
Download Phobos version 3.2.6 for Linux AMD 64
Download Phobos version 3.2.6 for Windows