If you use MCL software in your research, cite it as you would cite a
journal or a book. This includes papers published in regular or electronic
journals, usage of MCL as a back-end to a database that is accessible via a
web interface, or inclusion of MCL in a larger framework of software that is
distributed for other people to use. Include at least one of the following
citations:
Stijn van Dongen, Graph Clustering by Flow Simulation.
PhD thesis, University of Utrecht, May 2000.
( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )
Stijn van Dongen. A cluster algorithm for graphs. Technical Report
INS-R0010, National Research Institute for Mathematics and Computer
Science in the Netherlands, Amsterdam, May 2000.
( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )
and proper attributions to mcl's home http://micans.org/mcl/ and its author,
Stijn van Dongen. Do this *also* if you are using some wrapper around mcl
such as the blast module.
For biological applications, it is appropriate to cite, additionally,
the reference article for the first application of mcl to biological data:
Enright A.J., Van Dongen S., Ouzounis C.A.
An efficient algorithm for large-scale detection of protein families,
Nucleic Acids Research 30(7):1575-1584 (2002).
Please be advised that the TribeMCL module has been disabled. BLAST users
can use the blast package that is very well integrated with the core mcl
libraries and offers many options and extensive configurability. Use
mcxdeblast to parse BLAST files, use mcxassemble to transform the parser's
output to mcl input.
The Ensembl Families at ensembl.org are created with these programs.
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It is also possible to use the pipeline script mclblastline that
encapsulates mcxdeblast, mcxassemble, mcl, and clmformat (the latter
prettyprints clustering results).
Finally, with mcl's new label streaming facilities it is possible to cluster
directly from BLAST files. Refer to the mcl website for examples.
MCL documentation is in doc/, in various formats. It gets installed in
<prefix>/share/doc/mcl/. A few example input graphs are in graphs/, in the
mcl matrix format; these are installed in <prefix>/share/doc/mcl/examples/.
The MCL webpage is at http://micans.org/mcl/ .
MCL usage and development is discussed on the mcl-users mailing
list found at http://listserver.ebi.ac.uk/mailman/listinfo/mcl-users.
You can use this forum also for asking any MCL-related question.
The version tag, which is of the form dd-ddd, encodes the year and day in
year in which the distribution was made. So 02-058 encodes the 58-th day of
the year 2002.
Configure and compiler options
Synopsis
configure options:
--prefix=YOUR-PREFIX (e.g. $HOME/local)
--enable-blast
By default, MCL is compiled using C ints and floats -- the ints are used to
encode graph nodes/matrix indices, and the floats are used to encode edge
weights / matrix entries. These can be changed respectively to long and
double, by adding '-DINDEX_AS_LONG', and/or '-DVALUE_AS_DOUBLE' to the
CFLAGS environment variable. The first enables a possibly wider range of
indices to be used, the second increases the precision (which is presumably
not useful in the vast majority of cases). Using gcc under bash, you might
for example do
export CFLAGS='-g -O2 -Wall -ansi -pedantic -DVALUE_AS_DOUBLE'
before doing ./configure and make. If you are rebuilding, make sure to do
'make clean' first. You need not use doubles though; MCL does fine with
floats. These features (changing the basic types) have not yet been tested
thoroughly.
For enabling rudimentary runtime integrity checks, add -DRUNTIME_INTEGRITY.
MCL comes nowadays packaged with the BLAST parsing script mcxdeblast and the
pipeline script mclblastline. It encapsulates all the stages of parsing,
matrix creation, running mcl, and formatting the result into a single
application. Enable them by adding --enable-blast to ./configure.
These scripts can be used in place of the now disabled TribeMCL module.
See also
LICENSE for copyright and licensing, THANKS for contributors, INSTALL for
generic installation instructions.