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.TH "mcl" 7 "9 Oct 2022" "mcl 22-282" "MISCELLANEOUS "
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.SH NAME
mclfamily \- a description of the mcl family of cluster applications\&.

\fBmcl\fP is an implementation of the Markov Cluster Algorithm, aka MCL algoritm\&.
It is described in the \fBmcl manual\fP\&.
Several other applications are part of the MCL distribution\&. This manual pages
gives an overview\&.
.SH DESCRIPTION

.ZI 15m "\fBmcl(1)\fP"
the cluster algorithm
.in -15m
.ZI 15m "\fBmclfaq(7)\fP"
MCL Frequently Asked Questions
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.ZI 15m "\fBmcxio(5)\fP"
the network/matrix input/output format
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.ZI 15m "\fBmcx(1)\fP"
general network/matrix tasks
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.ZI 15m "\fBmcx\ \&diameter\fP"
compute diameter of an undirected network
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.ZI 15m "\fBmcx\ \&ctty\fP"
compute betweenness centrality
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.ZI 15m "\fBmcx\ \&clcf\fP"
compute clustering coefficient
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.ZI 15m "\fBmcx\ \&erdos\fP"
compute shortest paths in graphs
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.ZI 15m "\fBmcx\ \&query\fP"
analyse networks at different thresholds
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.ZI 15m "\fBmcx\ \&alter\fP"
apply network transformations
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.ZI 15m "\fBmcx\ \&convert\fP"
convert between interchange/binary storage types
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.ZI 15m "\fBmcxarray(1)\fP"
transform array data to MCL matrices
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.ZI 15m "\fBmcxdump(1)\fP"
dump a matrix optionally with label substitions
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.ZI 15m "\fBmcxload(1)\fP"
load label data into matrix and tab files
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.ZI 15m "\fBmcxrand(1)\fP"
randomly remove, add, and perturb edge weights
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.ZI 15m "\fBmcxmap(1)\fP"
relabel indices in a graph/matrix
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.ZI 15m "\fBmcxsubs(1)\fP"
extracting submatrices in various ways
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.ZI 15m "\fBmcxi(1)\fP"
general matrix operations
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.ZI 15m "\fBclm(1)\fP"
general graph-clustering related tasks
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.ZI 15m "\fBclm\ \&dist\fP"
compute split/join distance between clusterings
.in -15m
.ZI 15m "\fBclm\ \&vol\fP"
derive node volatility scores from a set of clusterings
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.ZI 15m "\fBclm\ \&info\fP"
compute performance measure for clusterings
.in -15m
.ZI 15m "\fBclm\ \&meet\fP"
compute intersection of clusterings
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.ZI 15m "\fBclm\ \&mate\fP"
find best matching clusters between clusterings
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.ZI 15m "\fBclm\ \&close\fP"
fetch connected components from graphs or subgraphs
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.ZI 15m "\fBclm\ \&imac\fP"
interpret MCL iterand/matrix as clustering
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.ZI 15m "\fBclm\ \&order\fP"
reorder indices to represent blocks from different clusterings
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.ZI 15m "\fBclm\ \&residue\fP"
extend subgraph clustering
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.ZI 15m "\fBmclblastline(1)\fP \fC*\fP"
BLAST pipeline
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.ZI 15m "\fBmcxdeblast(1)\fP \fC*\fP"
parse BLAST files
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Entries marked \fC*\fP are not available if only a default
install is done\&.