ELynx.Import.Tree.Newick

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

Code partly taken from Biobase.Newick.Import.

Specifications

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

Documentation

type Parser = Parsec Void ByteString

Shortcut.

Newick tree format

newick :: Parser (Tree (PhyloLabel ByteString))

Parse a single Newick tree. Also succeeds when more trees follow.

oneNewick :: Parser (Tree (PhyloLabel ByteString))

Parse a single Newick tree. Fails when end of file is not reached.

manyNewick :: Parser [Tree (PhyloLabel ByteString)]

Parse many Newick trees until end of file.

forest :: Parser [Tree (PhyloLabel ByteString)]

A forest is a set of trees separated by , and enclosed by parentheses.

leaf :: Parser (Tree (PhyloLabel ByteString))

A leaf is a node without children.

node :: Parser (PhyloLabel ByteString)

A node has a name and a branchLength.

name :: Parser ByteString

A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets (and commas).

branchLength :: Parser (Maybe Double)

Branch length.

Newick tree format with branch support as node names (e.g., used by IQ-TREE)

newickIqTree :: Parser (Tree (PhyloLabel ByteString))

IQ-TREE stores the branch support as node names after the closing bracket of a forest.

oneNewickIqTree :: Parser (Tree (PhyloLabel ByteString))

IQ-TREE stores the branch support as node names after the closing bracket of a forest.

manyNewickIqTree :: Parser [Tree (PhyloLabel ByteString)]

IQ-TREE stores the branch support as node names after the closing bracket of a forest.