SMORE: Synteny MOdulator of Repetitive Elements
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SMORE - Synteny Modulator of Repetitive Elements.

This is the readme to the SMORE pipeline, Synteny Modulator Of Repetitive Elements.

Usage: ./SMORE [general_options]

The general options are:

    --help|-h       print help page
    --version|-v    print version information
    --citation      print citation information
    --contact       print contact information
    --helpout       print explanation for structure and visualization of
                output files

For subcommands, use: ./SMORE 'subcommand' [options]

The SMORE subcommands are:

bake    The subcommand bake combines the subcommands prep and toast in
        order to easily start and run the pipeline completely. Hence,
        parameters for bake are the same as the combined parameters
        for prep and toast.

prep    This program will sort genetic elements in between genomic anchors
        based on MultiZ alignments. The genetic elements are
        taken from a list given as input or retrieved based on a covariance
        model as input for infernal.

toast   This program will take the prep-output and calculate the numbers
        for evolutionary events at the given phylogenetic tree.
        For a more detailed output, use --verbose or any combination
        of --clus, --graph, --aln. Please note that the verbose version
        might take significantly longer.

mix     This subcommand can be used after running SMORE prep. SMORE mix
        only produces a list of genetic clusters. This can be used to
        test different joining methods. Additionally, SMORE mix can split
        the number of clusters in several disjoint lists such that the
        succeeding subcommands can be run in parallel on the disjoint
        subsets to speed up running time of the program for large
        data sets. In case SMORE mix is splitting the list of clusters,
        it will output a command list that can be called to continue
        running the pipeline. The next subcommand to be called is
        SMORE roast.

roast   SMORE roast starts from a list of genetic clusters and will output
        lists of genetic events that can be further proceeded as an input
        for SMORE eat. SMORE roast can be used for large data sets in order
        to split and parallelize the process. The next subcommand in the
        pipeline will be SMORE eat.

eat     This subcommand is used after SMORE roast and will take list(s) of
        evolutionary events and output a phylogenetic tree with event and
        element counts. SMORE eat is able to summarize the outputs of
        parallelized runs such that all data is recombined at the
        phylogenetic tree.

For more details, please see the SMORE manual or the SMORE help pages.

For subcommands' help pages: ./SMORE 'subcommand' --help