.\" Copyright (c) 2022 Stijn van Dongen
.TH "mclindex" 7 "9 Oct 2022" "mclindex 22-282" "MISCELLANEOUS "
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.SH NAME
mclindex \- a list of the utilities and modules present in the MCL distribution\&.

For more information, consult \fBmclfamily(7)\fP\&.

.SH Generic stuff

.ZI 2m "\fBmcl(1)\fP"
\&
.br
the mcl manual page
.in -2m
.ZI 2m "\fBmclfaq(7)\fP"
\&
.br
the mcl FAQ
.in -2m
.ZI 2m "\fBmcxio(5)\fP"
\&
.br
the mcl matrix format specification
.in -2m
.ZI 2m "\fBmcx(1)\fP"
\&
.br
interface to basic matrix operations
.in -2m
.ZI 2m "\fBmcxdump(1)\fP"
\&
.br
dump matrices, optionally map indices to labels
.in -2m
.ZI 2m "\fBmcxarray(1)\fP"
\&
.br
transform array data to MCL matrices
.in -2m
.ZI 2m "\fBmcxconvert(1)\fP"
\&
.br
convert between ascii/binary storage types
.in -2m

.SH Dealing with clustering results

.ZI 2m "\fBclmdist(1)\fP"
\&
.br
compute distances between clusterings
.in -2m
.ZI 2m "\fBclminfo(1)\fP"
\&
.br
performance measures for clusterings
.in -2m
.ZI 2m "\fBclmmeet(1)\fP"
\&
.br
compute intersection of clusterings
.in -2m
.ZI 2m "\fBclmmate(1)\fP"
\&
.br
compute best matches between two clusterings
.in -2m
.ZI 2m "\fBclmimac(1)\fP"
\&
.br
Interpret Matrices (c\&.q\&. MCL iterands) As Clusterings
.in -2m
.ZI 2m "\fBclmresidue(1)\fP"
\&
.br
extend subgraph clusterings onto encompassing graph
.in -2m
.ZI 2m "\fBclmorder(1)\fP"
\&
.br
reorder indices to represent blocks from different clusterings
.in -2m
.ZI 2m "\fBclmclose(1)\fP"
\&
.br
fetch connected components from graphs or subgraphs
.in -2m

.SH Dealing with matrices

.ZI 2m "\fBmcxio(5)\fP"
\&
.br
the mcl matrix format specification
.in -2m
.ZI 2m "\fBmcx(1)\fP"
\&
.br
interface to basic matrix operations
.in -2m
.ZI 2m "\fBmcxsubs(1)\fP"
\&
.br
extract submatrices by specifying sets of nodes and clusters
.in -2m
.ZI 2m "\fBmcxmap(1)\fP"
\&
.br
remap matrix indices / relabel graph nodes
.in -2m