Man page - base_evolve(1)

Packages contains this manual

Package:  phast
apt-get install phast

Manuals in package:
• maf_parse(1)
• all_dists(1)
• exoniphy(1)
• base_evolve(1)
• draw_tree(1)
• refeature(1)
• phast(1)
• hmm_train(1)
• msa_view(1)
• stringiphy(1)
• msa_split(1)
• tree_doctor(1)
• convert_coords(1)
• hmm_tweak(1)
• hmm_view(1)
• dless(1)
• msa_diff(1)
• display_rate_matrix(1)
• clean_genes(1)
• prequel(1)
• eval_predictions(1)
Documentations in package:
• phast

Manual

BASE_EVOLVE

NAME
DESCRIPTION
EXAMPLE
OPTIONS

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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.

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