NAME

       base_evolve - Produce a synthetic alignment by simulating evolution according to

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.

EXAMPLE

              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.