---
name: "mclfamily"
section: "7"
platform: "linux"
package: "mcl-doc"
version: "1:22-282+ds-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mclfamily"
---

# mclfamily(7)

mclfamily - a description of the mcl family of cluster applications.

**mcl** is an implementation of the Markov Cluster Algorithm, aka MCL algoritm. It is described in the **mcl manual**. Several other applications are part of the MCL distribution. This manual pages gives an overview.

**[mcl(1)](/mcl/1.md)**  the cluster algorithm\
 **[mclfaq(7)](/mclfaq/7.md)**  MCL Frequently Asked Questions\
 **[mcxio(5)](/mcxio/5.md)**  the network/matrix input/output format\
 **[mcx(1)](/mcx/1.md)**  general network/matrix tasks\
 **mcx diameter**  compute diameter of an undirected network\
 **mcx ctty**  compute betweenness centrality\
 **mcx clcf**  compute clustering coefficient\
 **mcx erdos**  compute shortest paths in graphs\
 **mcx query**  analyse networks at different thresholds\
 **mcx alter**  apply network transformations\
 **mcx convert**  convert between interchange/binary storage types\
 **[mcxarray(1)](/mcxarray/1.md)**  transform array data to MCL matrices\
 **[mcxdump(1)](/mcxdump/1.md)**  dump a matrix optionally with label substitions\
 **[mcxload(1)](/mcxload/1.md)**  load label data into matrix and tab files\
 **[mcxrand(1)](/mcxrand/1.md)**  randomly remove, add, and perturb edge weights\
 **[mcxmap(1)](/mcxmap/1.md)**  relabel indices in a graph/matrix\
 **[mcxsubs(1)](/mcxsubs/1.md)**  extracting submatrices in various ways\
 **[mcxi(1)](/mcxi/1.md)**  general matrix operations\
 **[clm(1)](/clm/1.md)**  general graph-clustering related tasks\
 **clm dist**  compute split/join distance between clusterings\
 **clm vol**  derive node volatility scores from a set of clusterings\
 **clm info**  compute performance measure for clusterings\
 **clm meet**  compute intersection of clusterings\
 **clm mate**  find best matching clusters between clusterings\
 **clm close**  fetch connected components from graphs or subgraphs\
 **clm imac**  interpret MCL iterand/matrix as clustering\
 **clm order**  reorder indices to represent blocks from different clusterings\
 **clm residue**  extend subgraph clustering\
 **[mclblastline(1)](/mclblastline/1.md)** `*` BLAST pipeline\
 **[mcxdeblast(1)](/mcxdeblast/1.md)** `*` parse BLAST files

Entries marked `*` are not available if only a default install is done.