mclindex(7) MISCELLANEOUS mclindex(7)
NAME
mclindex - a list of the utilities and modules present in the MCL distribution.
For more information, consult mclfamily(7).
Generic stuff
mcl(1)
the mcl manual page
mclfaq(7)
the mcl FAQ
mcxio(5)
the mcl matrix format specification
mclpipeline(1)
generic pipeline (parsing/matrix creation/clustering/display)
mcx(1)
interface to basic matrix operations
mcxassemble(1)
prepare input matrix from cooccurrence scores
mcxdump(1)
dump matrices, optionally map indices to labels
mcxarray(1)
transform array data to MCL matrices
mcxconvert(1)
convert between ascii/binary storage types
Dealing with clustering results
clmformat(1)
display clusterings in browsable format
clmdist(1)
compute distances between clusterings
clminfo(1)
performance measures for clusterings
clmmeet(1)
compute intersection of clusterings
clmmate(1)
compute best matches between two clusterings
clmimac(1)
Interpret Matrices (c.q. MCL iterands) As Clusterings
clmresidue(1)
extend subgraph clusterings onto encompassing graph
clmorder(1)
reorder indices to represent blocks from different clusterings
clmclose(1)
fetch connected components from graphs or subgraphs
Dealing with matrices
mcxio(5)
the mcl matrix format specification
mcx(1)
interface to basic matrix operations
mcxsubs(1)
extract submatrices by specifiying sets of nodes and clusters
mcxmap(1)
remap matrix indices / relabel graph nodes
mcxassemble(1)
prepare input matrix from cooccurrence scores
Application specific parsers and wrappers
BLAST package - Documentation only available if installed with --enable-blast
__________________
mclblastline(1)
pipeline for clustering from blast files
mcxdeblast(1)
prepare input from blast files
mclindex 12-068 8 Mar 2012 mclindex(7)
Check Out this Related Man Page
clm mate(1) USER COMMANDS clm mate(1)
NAME
clm mate - compute best matches between two clusterings
clmmate is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode mate.
The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.
SYNOPSIS
clm mate [-o fname (output file name)] [-b (omit headers)] [--one-to-many (require multiple hits in <clfile1>)] [-h (print synopsis, exit)]
[--apropos (print synopsis, exit)] [--version (print version, exit)] <clfile1> <clfile2>
DESCRIPTION
clm mate computes for each cluster X in clfile1 all clusters Y in clfile2 that have non-empty intersection and outputs a line with the data
points listed below.
overlap(X,Y) # 2 * size(meet(X,Y)) / (size(X)+size(Y))
index(X) # name of cluster
index(Y) # name of cluster
size(meet(X,Y))
size(X-Y) # size of left difference
size(Y-X) # size of right difference
size(X)
size(Y)
projection(X, clfile2) # see below
projection(Y, clfile1) # see below
The projected size of a cluster X relative to a clustering K is simply the sum of all the nodes shared between any cluster Y in K and X,
duplications allowed. For example, the projected size of (0,1) relative to {(0,2,4), (1,4,9), (1,3,5)} equals 3.
The overlap between X and Y is exactly 1.0 if the two clusters are identical, and for nearly identical clusterings the score will be close
to 1.0.
All of this information can also be obtained from the contingency matrix defined for two clusterings. The [i,j] row-column entry in a con-
tigency matrix between to clusterings gives the number of entries in the intersection between cluster i and cluster j from the respective
clusterings. The other information is implicitly present; the total number of nodes in clusters i and j for example can be obtained as the
sum of entries in row i and column j respectively, and the difference counts can then be obtained by substracting the intersection count.
The contingency matrix can easily be computed using mcx; e.g.
mcx /clfile2 lm /clfile1 lm tp mul /ting wm
will create the contingency matrix in mcl matrix format in the file ting, where columns range over the clusters in clfile1.
The output can be put to good use by sorting it numerically on that first score field. It is advisable to use a stable sort routine (use the
-s option for UNIX sort) From this information one can quickly extract the closest clusters between two clusterings.
OPTIONS
-o fname (output file name)
Specify the name of the output file.
-b (omit headers)
Batch mode, omit column names.
--one-to-many (require multiple hits in <clfile1>)
Do not output information for clusters in the first file that are subset of a cluster in the second file.
AUTHOR
Stijn van Dongen.
SEE ALSO
mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
clm mate 12-068 8 Mar 2012 clm mate(1)