The clmimac manual

9 Nov 2004 clmimac 1.004, 04-314

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)] [-t num (tightness parameter)] [-tstep num (tightness step increment)] [-tbound num (tightness ceiling)] [--enstrict (remove overlap)] [--center (use center in defining tightness)] [-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.
-t num (tightness parameter)
|  | num should be a number in the range [0.0, 100.0]. The highter num, the less overlap will result. Its default value is 0. Multiple tightness parameters can be specified by using the -tstep option.
-tstep num (tightness step increment)
|  | Repeat interpretation for tightness parameters that increaes with stepsize num, starting with the value given by the -t option. By default, interpretation is not repeated.
-tbound num (tightness step increment)
|  | Ceiling for the tightness parameter as resulting from the -t and -tstep options.
--center (use center in defining tightness)
|  | This option will generally result in more stringent clusterings (containing fewer overlap), and tries to retain the most significant entries. Use this option only on matrices resulting from the MCL -dump dag option, and do not use it on matrices resulting from the -dump ite option.
-o fname (file name/stem)
|  | Write to file named fname. In case multiple tightness parameters are specified, use fname as stem for the output file names.
-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 mclfaq 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

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