MatrixMatchMaker version 2. Elisabeth Tillier, Robert L. Charleblois, Alexander Rodionov, Alexander Bezginov, Jonathan Rose. University of Toronto and University Health Network.
// This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version.
// This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details.
please cite:
Rodionov A., Bezginov A., Rose, J. and Tillier, ERM( 2011). A New, Fast Algorithm for Detecting Protein Coevolution using Maximum Compatible Cliques. Algorithms for Molecular Biology 6:17
Tillier ERM and R.L. Charlebois (2009) The Human Protein Coevolution Network. Genome Research. 19: 1861-1871.
Usage 1: ./mmmWithL -d1 distfile1 -d2 distfile2 -o outfile -a allowance [-brief] [-table [-top]] [-u] [-req reqTaxName] [-sz strictSize] [-rangeStart start -rangeEnd end] [-lower cutoffLower] [-upper cutoffUpper] [-aln2pmb] [-v] [-restore stateFileName] ...or... Usage 2: ./mmmWithL -b batchfile -o outfile -a allowance [-brief] [-u] [-req reqTaxName] [-sz strictSize] [-rangeStart start -rangeEnd end] [-lower cutoffLower] [-upper cutoffUpper] [-aln2pmb] [-v]
Required parameters:
-d1 distfile1 (if -b batchfile is not specified) Specifies the file name of the first distance matrix. -d2 distfile2 (if -b batchfile is not specified) Specifies the file name of the second distance matrix. -b batchfile (if -d1 distfile1 -d2 distfile2 are not specified) Specifies the name of a file containing tab-delimited pairs of distance matrix file names, one pair per line. -o outfile The desired name of the output file. -a allowance Specifies a value between 0.0 and 1.0, with smaller values requiring more precise matching, and larger values tolerating looser matching.
Optional parameters:
-brief Outputs a single tab-delimited line of output for the pair of distance matrices. -table (valid only when -b batchfile is not specified) Produces a tab-delimited matrix that lists the fit-weighted proportion of matches for each entry from the two distance matrices, over all common submatrices. For example, if seq1 matched seq2 in two of ten discovered submatrices, with a score of 0.8 and 0.9, respectively, then the entry for seq1_seq2 would be (0.8 + 0.9) / 10 = 0.17 -top (valid only when -table is specified) Restricts the -table output to just the best-scoring submatrix. -u Only attempts to match entries from the pair of distance matrices that have the same tag in their name. A tag ends with a pipe ("|") character, e.g. Ecoli in Ecoli|DnaA, or Hsapiens in Hsapiens|myc -req reqTaxName Requires that a submatrix include at least one entry with the specified reqTaxName, e.g. Hsapiens. -sz strictSize Returns common submatrices of size strictSize, if any. Does not attempt to find larger submatrices. -p distfileNamesPrefix The prefix is appended to the path of all distance matrices. -z Forces the output of zeros for combinations that have not reached the minSize (to be used in 'brief' mode). -minsize minSize Returns common submatrices of at least minSize, if any. Will not return smaller submatricies. Use this option to save memory with large matrices. -maxtrees maxTrees Limits the number of returned trees. Saves memory. -rangeStart start -rangeEnd end For distributed computing, launch this program multiple times with non-overlapping ranges, [start, end), start >= 0 and end <= distfile1's matrix size (auto-adjusted when -b is specified). Incompatible with -rndOrder. -quickmp If specified, the quickly but naively estimated match potential is included in batch output. -v Outputs the size of the largest common submatrix found so far, to stdout. -onlymp Does not perform MMM analysis, only prints MatchPotential (brief and MMML modes only). -restore stateFileName Resumes work from a previously interrupted MMM session -exacttime Do not round running time to nearest second, in brief mode -upper cutoffUpper All distances above cutoffUpper are set to zero. -lower cutoffLower All distances below cutoffLower are set to zero. -log Replaces the distances with their logs: dst=ln(dst)+1 if dst > 1. -noheader Omits the header from the output file (brief and MMML modes only). -onlyheader Prints the header to the output file and exits (brief and MMML modes only). -ignoreerrors Does not abort the run even in the case of program errors (intended for debugging only). -aln2pmb Enable recognition of .aln files as FASTA alignments and processing them into PMB matrices. Simply specify the alignment filename in place of distance matrix file. This works in both command-line and batch mode. A named alignment slice can be defined as comma-separated ranges of columns added after the filename. When using multiple ranges to define a slice, the ranges must go in increasing order, and must not overlap. An "inverse"slice (remove the slice itself and keep all other columns) can be specified by adding 'r' after the range. Do not use with multiple ranges. Format: |[range name]:-[r][,- ...] Examples: alignment1.aln alignment2.aln|pfam12820:373-546 alignment3.aln|disorder:16-90,150-150,430-519 alignment4.aln|:300-400r MMML extensions: -Lt rootedTreeFileName (required) File name for a Newick style tree file encompassing all of the taxa to be encountered in the MMM run. -LtopCov (optional) top-coverage style output. -Li ignoreTaxaFileName (optional) file listing taxon names to ignore in the MMML analysis. -Lb minBootstrapSupport (optional, default=1) an integer between 0 and 100 representing the threshold below which to collapse branches in parsing the treefile. -List (optional) if specified, lists the taxa in each clade in the output. -Lv (optional) if specified, outputs the clade sets.