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

# clmimac(1)

clm\_imac - Interpret Matrices (c.q. MCL iterands output by **mcl**) As Clusterings.

clmimac is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode *imac*. The options **-h**, **--apropos**, **--version**, **-set**, **--nop** are accessible in all **clm** modes. They are described in the **clm** manual page.

**clm imac** -imx \<fname\> \[options\]

**clm imac** **-imx** fname (*input file*) **\[-o** fname (*name/stem for output*)**\]** **\[-dag** fname (*output DAG*)**\]** **\[-overlap** str (*overlap mode*)**\]** **\[-sort** str (*size\|revsize\|lex\|none*)**\]** **\[-strict** num (*in 0..1*)**\]** **\[-h** (*print synopsis, exit*)**\]** **\[--apropos** (*print synopsis, exit*)**\]** **\[--version** (*print version, exit*)**\]**

Use **clm imac** to interpret matrices (as clusterings) output by **mcl** using **mcl**'s **-dump** **ite** option.

Use **clm imac** only if you have a special reason; the normal usage of **mcl** is to do multiple runs for varying **-I** parameters and use the clusterings output by **mcl** itself. One reason is if you are interested in clusterings with overlap; early MCL iterands generally induce clusterings possessing overlap. Another reason is to investigate how the cluster structure associated with the MCL process evolves over time.

**-imx** fname (*input file*)\
 The input file is presumably an MCL iterand resulting from the mcl option **-dump** **ite**.

**-strict** num (*in 0..1*)\
 Higher values (up until 1) will thin out the DAG constructed by **clm imac**. The default value is 0.00001, yielding the full DAG.

**-o** fname (*file name/stem*)\
 Write to file named *fname*.

**-dag** fname (*output DAG*)\
 Write the DAG (directed acyclic graph) constructed from the input to file. This DAG is constructed according to the structure associated with diagonally positive semi-definite matrices as described in the PhD thesis *Graph clustering by flow simulation*. Consult **[mclfamily(7)](/mclfamily/7.md)** for references.

**-sort** str (*size\|revsize\|lex\|none*)\
 Sort the clusters either by increasing size, decreasing size, lexicographically by the indices they contain, or use the clustering exactly as obtained from the interpretation routine.

**-overlap** mode (*overlap mode*)\
 With *mode* set to *cut*, remove any overlap by allocating the nodes in overlap to the first cluster in which they were found. Mode *keep* leaves overlap unchanged, and mode *split* results in overlapping parts excised and introduced as clusters in their own right.

Stijn van Dongen.

**[mclfamily(7)](/mclfamily/7.md)** for an overview of all the documentation and the utilities in the mcl family.