PROGRAM: base_evolve

USAGE: base_evolve [file.hmm] tree1.mod [tree2.mod tree3.mod ...] > alignment

DESCRIPTION: 

    Produce a synthetic alignment by simulating evolution according to
    a phylogenetic model or a phylo-HMM.  Deals with base-substitution
    only, not indels.  If a multiple tree models are given, then an
    HMM file must be given showing how to transition between them.

EXAMPLES:

    base_evolve --nsites 500 mytree.mod > simulated.fa

    base_evolve --nsites 500 simple-gene.hmm tree1.mod tree2.mod \
        tree3.mod --features simulated2.gff --catmap simple-gene.cm \
        > simulated2.fa

OPTIONS:

    --nsites, -n <nsites>
        Generate an alignment with <nsites> columns.  Default is 1000.

    --msa-format, -o FASTA|PHYLIP|MPM|SS
        Output alignment in specified format.  Default is FASTA.

    --features, -f <out.gff>
        (for use with a phylo-HMM)  Output an annotations file in GFF
        reflecting the path through the phylo-HMM.

    --catmap, -c <map.cm>
        (for use with --features)  Use specified category map to
        define feature names.

    --embed, -e <alt.mod>,<length>
        Embed an artificial element of the given length in the alignment,
        drawing columns from <alt.mod>.  A single element is embedded in
        the exact middle of the generated alignment.  Useful for testing
        sensitivity of methods for functional element detection.

    --help, -h
        Display this help message and exit.