MCL implements Markov cluster algorithm. Among its applications is the assignment of proteins into families based on precomputed sequence similarity information. This approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins.

References:

• Stijn van Dongen
  Graph Clustering by Flow Simulation
  PhD thesis, University of Utrecht, May 2000.
• Enright A.J., Van Dongen S., Ouzounis C.A.
  An efficient algorithm for large-scale detection of protein families,
  Nucleic Acids Research30(7):1575-1584 (2002).

• MCL Home page
• MCL Github page

• Module Name: MCL (see the modules page for more information)
• Unusual environment variables set
  • MCL_HOME  installation directory
  • MCL_BIN       executable directory
  • MCL_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3200 ~]$ module load mcl 
[+] Loading MCL 14-137  ...
[user@cn3200 ~]$ cp $MCL_DATA/* .
[user@cn3200 ~]$ mcl cathat  --abc -o out2.cathat 
[mcl] new tab created
[mcl] pid 10660
 ite ------  chaos  time hom(avg,lo,hi) m-ie m-ex i-ex fmv
  1  ......   0.47  0.00 0.87/0.80/0.95 1.33 1.33 1.33 100
  2  ......   0.53  0.00 0.86/0.69/0.95 1.24 1.21 1.67 100
  3  ......   0.35  0.00 0.95/0.88/1.00 1.00 0.67 1.14 100
  4  ......   0.44  0.00 0.94/0.88/1.00 1.08 0.68 0.81 100
  5  ......   0.24  0.00 0.89/0.78/1.00 1.17 0.67 0.57 100
  6  ......   0.20  0.00 0.89/0.80/0.99 0.92 0.92 0.57 100
  7  ......   0.12  0.00 0.95/0.95/0.95 0.92 0.92 0.57 100
  8  ......   0.20  0.00 0.92/0.85/1.00 0.92 0.92 0.57 100
  9  ......   0.25  0.00 0.88/0.76/1.00 0.92 0.69 0.43 100
 10  ......   0.15  0.00 0.93/0.85/1.00 0.90 0.90 0.43 100
 11  ......   0.02  0.00 0.99/0.98/1.00 0.90 0.90 0.43 100
 12  ......   0.00  0.00 1.00/1.00/1.00 0.90 0.90 0.43 100
 13  ......   0.00  0.00 1.00/1.00/1.00 0.90 0.60 0.29 100
[mcl] jury pruning marks: <100,99,99>, out of 100
[mcl] jury pruning synopsis: <99.6 or perfect> (cf -scheme, -do log)
[mcl] output is in out.cathat
[mcl] 2 clusters found
[mcl] output is in out.cathat
...
...

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$