NAME¶

mclfamily - a description of the mcl family of cluster applications. mcl is an implementation of the Markov Cluster Algorithm, aka MCL algoritm. It is described in the mcl manual. Several other applications are part of the MCL distribution. This manual pages gives an overview.

DESCRIPTION¶

mcl(1) the cluster algorithm

mclfaq(7) MCL Frequently Asked Questions

mcxio(5) the network/matrix input/output format

mcx(1) general network/matrix tasks

mcx diameter compute diameter of an undirected network

mcx ctty compute betweenness centrality

mcx clcf compute clustering coefficient

mcx erdos compute shortest paths in graphs

mcx query analyse networks at different thresholds

mcx alter apply network transformations

mcx convert convert between interchange/binary storage types

mcxarray(1) transform array data to MCL matrices

mcxdump(1) dump a matrix optionally with label substitions

mcxload(1) load label data into matrix and tab files

mcxrand(1) randomly remove, add, and perturb edge weights

mcxmap(1) relabel indices in a graph/matrix

mcxsubs(1) extracting submatrices in various ways

mcxi(1) general matrix operations

mcxassemble(1) create matrices from raw data

clm(1) general graph-clustering related tasks

clm dist compute split/join distance between clusterings

clm vol derive node volatility scores from a set of clusterings

clm info compute performance measure for clusterings

clm meet compute intersection of clusterings

clm mate find best matching clusters between clusterings

clm close fetch connected components from graphs or subgraphs

clm imac interpret MCL iterand/matrix as clustering

clm order reorder indices to represent blocks from different clusterings

clm residue extend subgraph clustering

clmformat(1) display clusters as html or txt files

mclpipeline(1) parsing/assembly/clustering/display

mclblastline(1) * BLAST pipeline

mcxdeblast(1) * parse BLAST files
Entries marked * are not available if only a default install is done.