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 Generate an alignment with columns. Default is 1000. --msa-format, -o FASTA|PHYLIP|MPM|SS Output alignment in specified format. Default is FASTA. --features, -f (for use with a phylo-HMM) Output an annotations file in GFF reflecting the path through the phylo-HMM. --catmap, -c (for use with --features) Use specified category map to define feature names. --embed, -e , Embed an artificial element of the given length in the alignment, drawing columns from . 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.