New upstream version 3.1.5+dfsg (e7366411) · Commits · Debian Med / bali-phy

doc/README.itex.xml

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		<!DOCTYPE book [
		<!ENTITY version "3.1" >
		<!ENTITY version "3.1.4" >

		<!ENTITY source.file "bali-phy-&version;.tar.gz" >
		<!ENTITY linux64.file "bali-phy-&version;-linux64.tar.gz" >
		@@ -161,7 +161,8 @@ However, note that this might conflict with R installed from other places, such

		<section><info><title>Install on Linux</title></info>

		<section><info><title>Install BAli-Phy using <command>apt-get</command> (recommended if using <emphasis>Debian: testing or unstable</emphasis>)</title></info>
		<section><info><title>Install BAli-Phy using <command>apt-get</command></title></info>
		BAli-Phy is available on Ubuntu <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://launchpad.net/ubuntu/+source/bali-phy/">("Cosmic Cuttlefish" or later)</link>, and Debian (<link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://packages.debian.org/search?keywords=bali-phy&searchon=names&section=all">testing and unstable</link>).
		<screen><prompt>%</prompt> <userinput>sudo apt-get install bali-phy</userinput></screen>
		Check that the executable runs:
		<screen><prompt>%</prompt> <userinput>bali-phy --version</userinput></screen>

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		% tree-tool(1)
		% Benjamin Redelings
		% Feb 2018

		# NAME

		tree-tool -- Perform various operations on Newick trees.

		# SYNOPSIS

		tree-tool _tree-file_ [OPTIONS]

		# DESCRIPTION

		Perform various operations on Newick trees.

		# GENERAL OPTIONS:
		-h, --help
		: produce help message

		-v, --verbose
		: Output more log messages on stderr.

		--prune _arg_
		: Comma-separated taxa to remove

		--resolve
		: Comma-separated taxa to remove


		# REPORTING BUGS:
		BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

		Please send bug reports to <bali-phy-users@googlegroups.com>.

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		{
		"name": "Frequencies.uniform",
		"result_type": "List[Pair[String,Double]]",
		"call": "SModel.uniform_frequencies[a]",
		"args": [
		{
		"arg_name": "a",
		"arg_type": "a",
		"default_value": "getAlphabet"
		}
		],
		"examples": ["hky85[pi=Frequencies.uniform]"]
		}

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		@@ -30,5 +30,13 @@
		],
		"title": "Free rates model",
		"description":"Rate heterogeneity model where the rate and frequency of each category can be estimated from the data.",
		"examples": ["hky85+Rates.free[n=3]"]
		"examples": ["hky85+Rates.free[n=3]"],
		"citation":{"type": "article",
		"title": "A space-time process model for the evolution of DNA sequences.",
		"year": "1995",
		"author": [{"name": "Yang, Ziheng"}],
		"journal": {"name": "Genetics", "volume": "139", "number": "2", "pages": "993--1005"},
		"identifier": [{"type":"pmid","id":"7713447"},
		{"type":"pmcid","id":"PMC1206396"}]
		}
		}

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		{
		"arg_name": "omega",
		"arg_type": "Double",
		"default_value": "~uniform[0,1]"
		"default_value": "~uniform[0,1]",
		"description": "Excess dN/dS"
		},
		{
		"arg_name": "w",
		"arg_type": "List[Pair[String,Double]]",
		"default_value": "zip[letters[A],~iid[length[letters[A]],log_normal[0,0.5]]]"
		"default_value": "zip[letters[A],~iid[length[letters[A]],log_normal[0,0.5]]]",
		"description": "Fitness of codons"
		},
		{
		"arg_name": "submodel",
		"arg_type": "RevCTMC[a]",
		"default_value": "hky85_sym",
		"alphabet": "getNucleotides[A]"
		"default_value": "hky85",
		"alphabet": "getNucleotides[A]",
		"description": "Model of neutral nucleotide substitution"
		},
		{
		"arg_name": "A",
		"arg_type": "Codons[a]",
		"default_value": "getAlphabet"
		"default_value": "getAlphabet",
		"description": "The alphabet"
		}
		],
		"extract": "all"
		"extract": "all",
		"citation":{"type": "article",
		"title": "Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage",
		"year": "2008",
		"author": [{"name": "Yang, Ziheng"},{"name": "Nielsen, Rasmus"}],
		"journal": {"name": "Molecular Biology and Evolution", "volume": "25", "number": "3", "pages": "568--579"},
		"identifier": [{"type":"doi","id":"10.1093/molbev/msm284"}]
		}
		}