The clmimac manual

27 Feb 2006 clmimac 1.006, 06-058

1. |  | NAME
2. |  | SYNOPSIS
3. |  | DESCRIPTION
4. |  | OPTIONS
5. |  | AUTHOR
6. |  | SEE ALSO

## NAME

clmimac - Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

## SYNOPSIS

clmimac -imx <fname> [options]

clmimac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output DAG)] [--enstrict (remove overlap)] [-sort str (size|revsize|lex|none)] [-h (list help)] [--apropos (list synopsis of all options)]

## DESCRIPTION

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

Use clmimac 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.

## OPTIONS

-imx fname (input file)
|  | The input file is presumably an MCL iterand resulting from the mcl option -dump ite.
-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 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.
--enstrict (remove overlap)
|  | Remove overlap should it be found, by allocating the nodes in overlap to the first cluster in which they were found.
-h (list help)
|  | Print help, this could possibly be the same output as supplied with --apropos.
--apropos (list synopsis of all options)
|  | List a one-line synopsis for all options.

## AUTHOR

Stijn van Dongen.

## SEE ALSO

mclfamily for an overview of all the documentation and the utilities in the mcl family.