tlynx-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

TLynx.Parsers

Description

Creation date: Wed Apr 22 13:34:35 2020.

Synopsis

Documentation

parseTree :: NewickFormat -> FilePath -> IO (Tree Phylo Name) Source #

Parse a Newick tree file or a Nexus file with Newick trees.

Error if no or more than one trees are found. Error if both file formats fail to parse.

parseTrees :: NewickFormat -> FilePath -> IO (Forest Phylo Name) Source #

Parse a Newick tree file or a Nexus file with Newick trees.

Error if both file formats fail to parse.

data NewickFormat #

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.

Instances

Instances details
FromJSON NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

ToJSON NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Bounded NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Enum NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Generic NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Associated Types

type Rep NewickFormat :: Type -> Type #

Read NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Show NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

Eq NewickFormat 
Instance details

Defined in ELynx.Tree.Import.Newick

type Rep NewickFormat 
Instance details

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)))

newickHelp :: [String] Source #

Help for different NewickFormats.