elynx-tree-0.7.2.2: Handle phylogenetic trees
Copyright2021 Dominik Schrempf
LicenseGPL-3.0-or-later
Maintainerdominik.schrempf@gmail.com
Stabilityunstable
Portabilityportable
Safe HaskellSafe-Inferred
LanguageHaskell2010

ELynx.Tree.Import.Newick

Description

Creation date: Thu Jan 17 14:56:27 2019.

Some functions are inspired by Biobase.Newick.Import.

Specifications

In particular, no conversion from _ to (space) is done right now.

For a description of rooted Trees, please see the Rooted

Synopsis

Documentation

data NewickFormat Source #

Newick tree format.

  • Standard: Branch support values are stored in square brackets after branch lengths.
  • IqTree: Branch support values are stored as node names after the closing bracket of forests.
  • RevBayes: Key-value pairs are provided in square brackets after node names as well as branch lengths. NOTE: Key value pairs are ignored.

Constructors

Standard 
IqTree 
RevBayes 

Instances

Instances details
FromJSON NewickFormat Source # 
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Defined in ELynx.Tree.Import.Newick

ToJSON NewickFormat Source # 
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Bounded NewickFormat Source # 
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Enum NewickFormat Source # 
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Generic NewickFormat Source # 
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Associated Types

type Rep NewickFormat :: Type -> Type #

Read NewickFormat Source # 
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Show NewickFormat Source # 
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Eq NewickFormat Source # 
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type Rep NewickFormat Source # 
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Defined in ELynx.Tree.Import.Newick

type Rep NewickFormat = D1 ('MetaData "NewickFormat" "ELynx.Tree.Import.Newick" "elynx-tree-0.7.2.2-7v79cynrH4qIkHZDd1p2Yg" 'False) (C1 ('MetaCons "Standard" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "IqTree" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "RevBayes" 'PrefixI 'False) (U1 :: Type -> Type)))

newick :: NewickFormat -> Parser (Tree Phylo Name) Source #

Newick tree parser. Also succeeds when more trees follow.

oneNewick :: NewickFormat -> Parser (Tree Phylo Name) Source #

One Newick tree parser. Fails when end of input is not reached.

someNewick :: NewickFormat -> Parser (Forest Phylo Name) Source #

One or more Newick trees parser.