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seqMMLigner: SEQuence Minimum Message Length aLIGNER of proteins
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** COMPILATION **
  cd <path/to/>seqmmligner_2.5-1/
  make

** EXECUTION **
To compare two amino acid sequences:
  ./bin/seqmmligner <seq1 fasta> <seq2 fasta> [OPTIONS]

To evaluate the fitness (compression) given any sequence alignment:
  ./bin/seqmmligner --ivalue <alignment fasta>)

To compute the expected inter-alignment distance between given sequences 
and a reference alignment:
  ./bin/seqmmligner <seq1 fasta> <seq2 fasta> --expalgndist <reference alignment fasta>

** OPTIONS **
   --criterion <mode>
     modes:
     * 'optimal' (default) computes the optimal alignment maximizing the
        joint probability.
     * 'marginal' computes the (negative log) marginal probability of
        the sequence relationship.
     * 'marginal-interactive' computes same as above, but in an interactive
        mode of operation

   -o  <output_prefix_string>
      outputs all files generated by the program with this prefix
      
   --matrix <type>
    Types:
     * MMLSUM (default) 
     * PFASUM 
     * VTML 
     * BLOSUM
     * LG 
     * JTT
     * MIQS
     * WAG
     * JO
     * PAM


** REFERENCES **
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SeqMMLigner reference (describing the MML framework and optimal/marginal modes)
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Dinithi Sumanaweera, Lloyd Allison, and Arun S Konagurthu 
  Statistical compression of protein sequences and inference of marginal
  probability landscapes over competing alignments using finite state models
  and Dirichlet priors.
Bioinformatics, Volume 35, Issue 14, July 2019, Pages i360–i369
DOI:https://doi.org/10.1093/bioinformatics/btz368
Project webpage: https://lcb.infotech.monash.edu/seqmmligner/
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Time parameterized models reference (supporting --matrix option)
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Dinithi Sumanaweera, Lloyd Allison, and Arun S Konagurthu
  Bridging the gaps in statistical models of protein alignment 
(in communication)
ArXiv link to the manuscript: https://arxiv.org/abs/2010.00855
Project Webpage: https://lcb.infotech.monash.edu/mmlsum/
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Expected inter-alignment distance reference (supporting '--expalgndist' option)
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Sandun Rajapaksa, Dinithi Sumanaweera, Arthur Lesk, Lloyd Allison, 
Peter J. Stuckey, Maria Garcia de la Banda, David Abramson,  and 
Arun S. Konagurthu 
  On the reliability and the limits of inference of amino acid sequence 
  alignments 
(in communication)
Project webpage: https://lcb.infotech.monash.edu/ead/
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** CONTACT **
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Arun Konagurthu <arun.konagurthu@monash.edu>
Dinithi Sumanaweera <dinithi.sumanaweera@monash.edu>
Sandun Rajapaksa    <sandun.rajapaksa@monash.edu>
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