Man page - indelfit(1)

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

INDELFIT

NAME
DESCRIPTION
OPTIONS

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NAME

indelFit - Estimate the parameters of a simple indel model, given an indel history

DESCRIPTION

Estimate the parameters of a simple indel model, given an indel history and a tree. By default, writes estimates of three parameters to stdout: an insertion rate alpha, a deletion rate beta, and a parameter tau roughly equal to the inverse of the expected indel length (modulo adjustments required to make probabilities sum to one).

An indel history can be obtained with indelHistory and a tree with phyloFit.

OPTIONS

--alpha , -a <val>

Starting value of alpha, the insertion rate.

Default is 0.02.

	--beta , -b <val> Starting value of beta, the deletion rate. Default is 0.04.
	--tau , -t <val> Starting value of tau, the length parameter. Default is 0.05.
	--lnl , -L

Compute log likelihood of model only, without optimizing parameters. The options above can be used to set the parameters as desired.

--columns , -c

Output log likelihood of each column.

--features , -f <file.gff>

Estimate separate parameters for each type of feature in the given file, as well as for background sites.

--reference , -r <name>

(For use with --features ) Name of species (node of tree) defining coordinate frame of features. By default, the coordinate frame of the entire alignment is assumed.

--log , -l <file>

Write log of optimization to specified file.

--help , -h

Display this help message and exit.

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