Markov CLustering or the Markov CLuster algorithm, MCL is a method for clustering weighted or simple networks, a.k.a. graphs. It is accompanied in this source code by other network construction and (trait) analysis programs.
MCL has been used a lot in the field of bioinformatics, starting with the TribeMCL method published by Enright, van Dongen and Ouzounis. A lot (too much) of information and documentation is available at micans.org .
This is the name I use sometimes to refer to the collection of sibling programs to MCL for network and matrix loading, filtering and subsetting, including computation of network traits such as centrality and clustering coefficient.
The program MCL has been very stable or nearly unchanging for well over 15
years now, with the last speed optimisations occurring about a decade ago. I
aim to do some development in its sibling programs, including improving those
that implement (currently somewhat inelegant) mini-formats such as mcx alter
and mcxsubs.
A second are of development, tied to the first, will be low-level fast loading, filtering and subsetting of large networks and matrices. I have found occasional use for this in past projects, and under certain conditions an mcl-edge recipe, if possible, will be a few times faster than a recipe using Python panda or R. Challenge of this type are sometimes a reason to expand mcl-edge's capabilities.
Another reason for new releases is that new compilers and compiler settings have unearthed two or three blemishes in the code base that needed fixing.
Currently only development MCL releases have been made available from this repository. Stable releases will follow in the not too distant future. This code needs the C library in the github repo micans/cimfomfa, hence the build procedure has been changed somewhat and needs more steps.
- This script will pull http://micans.org/mcl/dev/mcl-21-257.tar.gz and http://micans.org/dev/cimfomfa-21-257.tar.gz and then (attempt to) build an mcl release.
- installmcl.sh is similar with a little more control and needs local tar archives, for example the two listed above.
I aim to make a new release, the first since mcl-14-137 (released at about day 137 in the year 2014), in autumn 2021. A development release (mcl-21-257) is available, please have a look at the dev branch.
If you have suggestions please get in touch or open an issue.