Man page - makehky(1)

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Package:  phast
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• maf_parse(1)
• all_dists(1)
• exoniphy(1)
• base_evolve(1)
• draw_tree(1)
• refeature(1)
• phast(1)
• hmm_train(1)
• msa_view(1)
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• msa_split(1)
• tree_doctor(1)
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• hmm_tweak(1)
• hmm_view(1)
• dless(1)
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• eval_predictions(1)
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Manual

MAKEHKY

NAME
DESCRIPTION
OPTIONS

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NAME

makeHKY - Generates an HKY tree model, given kappa (the transition/transversion

DESCRIPTION

Generates an HKY tree model, given kappa (the transition/transversion rate ratio). The equilibrium base composition and either a branch length or a complete tree can be specified by the options described below.

OPTIONS

--gc , -g <val>

Define base composition according to specified G+C composition, assuming P(A)=P(T) and P(C)=P(G). Default is 0.4.

	--pi , -p <pi_A,pi_C,pi_G,pi_T> Override --gc and define base composition explicitly. Values will be renormalized to ensure they sum exactly to one.
	--branch-length , -t <val>

Assume a tree consisting of a single branch of specified length. Default value is 1.

	--tree , -T <tree.nh> Override --branch-length and use specified tree.
	--help , -h

Display this help message and exit.

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