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.