bin/mcmusec 
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Usage: mcmusec -f <ptt file list> [-q <query gc list>] -s <minsize> -g <bp|gi> -d <maxgap> -k <minsup> [-o <output: optional>] [-n <simple output: optional>] [-v]

-v: output the number of gene clusters per size in console [false]
-s: minimal COG number in gene clusters [2]
-d: unified maxgap for all genomes [1000]
-g: maxgap in base pair (bp) or gene insertions (gi) [bp]
-k: minimal number of genomes where the gene clusters occur [2] 
-f: the file with a list of input genomes' ptt file names (or filename <space> maxgap, if -d is not used), one per line
-q: query the list of gene clusters (cog names seperated by space), one per line, optional
-o: output file, optional, [output.mc]
-n: simple output file, optional, [output.mcs]

Example:
1.	bin/mcmusec -f data/Francesca_Science06_133_genomes.path.txt -g gi -d 2 -k 3 -o result/Francesca_Science06_133_genomes/output_gi_d2_k3.mc -n result/Francesca_Science06_133_genomes/output_gi_d2_k3.mcs
will output all max-gap clusters in the genomes listed at data/Francesca_Science06_133_genomes.path.txt, with minsize=2, maxgap=2gi, minsupp=3, to file result/Francesca_Science06_133_genomes/output_gi_d2_k3.mc. The file result/Francesca_Science06_133_genomes/output_gi_d2_k3.mcs contains the same results but in a :-deliminated-column format with summarized information only.

2.	bin/mcmusec -f data/Francesca_Science06_133_genomes.path.txt -q data/RegulonDB_operon.cog -g gi -d 2 -o result/RegulonDB_operon/operon_gi_d2.mc -n result/RegulonDB_operon/operon_gi_d2.mcs
will scan the known operons' COGs at data/RegulonDB_operon.cog, and output all occurrences in the genomes listed at data/Francesca_Science06_133_genomes.path.txt, with maxgap=2gi, to file result/RegulonDB_operon/operon_gi_d2.mc. The file result/RegulonDB_operon/operon_gi_d2.mcs contains the same results but in a :-deliminated-column format with summarized information only.


bin/bls
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Usage: bls <tree file> <map file> <cluster result file> <output file>

Exmaple:
bin/bls data/tree_Feb15_midpoint_rooted.txt data/Francesca_Science06_133_genomes.info.txt result/RegulonDB_operon/operon_gi_d2.mcs result/RegulonDB_operon/operon_gi_d2.bls
will compute bls for the clusters in result/RegulonDB_operon/operon_gi_d2.mcs, using the phylogeny at data/tree_Feb15_midpoint_rooted.txt and the mapping of tax ID (column 1) to NCBI's sequence accession ID (column 2) at data/Francesca_Science06_133_genomes.info.txt, output the bls as an additional column to the input cluster file to file result/RegulonDB_operon/operon_gi_d2.bls


bin/randomsample
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Usage: randomesample -f [ptt path file] -s [cluter size] -g [bp|gi] -d [maxgap] -r [number of samples]

Example:
bin/randomsample -f data/Francesca_Science06_133_genomes.path.txt -s result/RegulonDB_operon/operon_gi_d2.gcs -g gi -d 2 -r 1000
will randomly sample 1000 clusters for each genome-size pair listed at result/RegulonDB_operon/operon_gi_d2.gcs, output to defaut file: NC_#.rdm where NC_# is the NCBI's sequence accession ID, for each input genome.


bin/getClusterSizes.pl
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Usage: getClusterSizes.pl <mcsFile> > output

Example:
bin/getClusterSizes.pl result/RegulonDB_operon/operon_gi_d2.mcs > result/RegulonDB_operon/operon_gi_d2.gcs
will scan the result file result/RegulonDB_operon/operon_gi_d2.mcs to compute the obtained gene clusters' size for each genome, output to file result/RegulonDB_operon/operon_gi_d2.gcs

Note:
This output will be used later to randomly sample clusters for each genome-size pair.


bin/cmptBLSpval.pl
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Usage: cmptBLSpval.pl <mcsFile> <rdmMcsDir> > output

Example:
bin/cmptBLSpval.pl result/RegulonDB_operon/operon_gi_d2.bls result/RegulonDB_operon/rdm_gi_d2_bls > result/RegulonDB_operon/operon_gi_d2.pval
will compute the p-value for obtained clusters at result/RegulonDB_operon/operon_gi_d2.bls based on the randomly sampled clusters' bls distribution files in the folder result/RegulonDB_operon/rdm_gi_d2_bls, output the result p-value as an additional column to the input cluster bls file to file result/RegulonDB_operon/operon_gi_d2.pval