ELynx.Data.Tree.Phylogeny

Creation date: Thu Jan 17 16:08:54 2019.

A phylogeny is a Tree with unique leaf labels, and the order of the trees in the sub-forest is considered to be meaningless.

Internally, however, the underlying Tree data structure stores the sub-forest as a list, which has a specific order. Hence, we have to do some tricks when comparing trees, and tree comparison is slow.

Also, the uniqueness of the leaves is not ensured by the data type, but has to be checked at runtime. Functions relying on the tree to have unique leaves do perform this check, and return Left with an error message, if the tree has duplicate leaves.

Note: Trees are rooted.

Note: Trees encoded in Newick format correspond to rooted trees. By convention only, a tree parsed from Newick format is usually thought to be unrooted, when the root node is multifurcating and has three children. This convention is not enforced here. Newick trees are just parsed as they are, and a rooted tree is returned.

The bifurcating root of a tree can be changed with roots, or rootAt.

Trees with multifurcating root nodes can be properly rooted using outgroup.

Functions

equal :: (Eq e, Eq a) => Tree e a -> Tree e a -> Bool

The equality check is slow because the order of children is considered to be arbitrary.

intersect :: (Semigroup e, Eq e, Ord a) => Forest e a -> Either String (Forest e a)

Compute the intersection of trees.

The intersections are the largest subtrees sharing the same leaf set.

Degree two nodes are pruned with prune.

Return Left if: - the intersection of leaves is empty.

bifurcating :: Tree e a -> Bool

Check if a tree is bifurcating.

A Bifurcating tree only contains degree one (leaves) and degree three nodes (internal bifurcating nodes).

outgroup :: (Semigroup e, Splittable e, Ord a) => Set a -> a -> Tree e a -> Either String (Tree e a)

Resolve a multifurcation at the root using an outgroup.

A bifurcating root node with the provided label is introduced. The affected branch is split.

Note, the degree of the former root node is decreased by one.

If the root node is bifurcating, use rootAt.

Return Left if - the tree has duplicate leaves; - the root node is not multifurcating; - the provided outgroup is not found on the tree or is polyphyletic.

midpoint :: (Semigroup e, Splittable e, Measurable e) => Tree e a -> Either String (Tree e a)

Root tree at the midpoint.

Return Left if - the root node is not bifurcating.

roots :: (Semigroup e, Splittable e) => Tree e a -> Either String (Forest e a)

For a rooted tree with a bifurcating root node, get all possible rooted trees.

The root node is moved.

For a tree with l=2 leaves, there is one rooted tree. For a bifurcating tree with l>2 leaves, there are (2l-3) rooted trees. For a general tree with a bifurcating root node, and a total number of n>2 nodes, there are (n-2) rooted trees.

Moving a multifurcating root node to another branch would change the degree of the root node. Hence, a bifurcating root is required. To resolve a multifurcating root, please use outgroup.

Connect branches according to the provided Semigroup instance.

Upon insertion of the root, split the affected branch into one out of two equal entities according to a given function.

Return Left if the root node is not bifurcating.

rootAt :: (Semigroup e, Splittable e, Eq a, Ord a) => Bipartition a -> Tree e a -> Either String (Tree e a)

Root a tree at a specific position.

Root the tree at the branch defined by the given bipartition. The original root node is moved to the new position.

The root node must be bifurcating (see roots and outgroup).

Connect branches according to the provided Semigroup instance.

Upon insertion of the root, split the affected branch according to the provided Splittable instance.

Return Left, if: - the root node is not bifurcating; - the tree has duplicate leaves; - the bipartition does not match the leaves of the tree.

Branch labels

data Phylo

Branch label for phylogenetic trees.

Branches may have a length and a support value.

Constructors

Phylo

Fields

• brLen :: Maybe BranchLength
• brSup :: Maybe BranchSupport

Instances

Eq Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

(==) :: Phylo -> Phylo -> Bool

(/=) :: Phylo -> Phylo -> Bool

Ord Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

compare :: Phylo -> Phylo -> Ordering

(<) :: Phylo -> Phylo -> Bool

(<=) :: Phylo -> Phylo -> Bool

(>) :: Phylo -> Phylo -> Bool

(>=) :: Phylo -> Phylo -> Bool

max :: Phylo -> Phylo -> Phylo

min :: Phylo -> Phylo -> Phylo

Read Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

readsPrec :: Int -> ReadS Phylo

readList :: ReadS [Phylo]

readPrec :: ReadPrec Phylo

readListPrec :: ReadPrec [Phylo]

Show Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

showsPrec :: Int -> Phylo -> ShowS

show :: Phylo -> String

showList :: [Phylo] -> ShowS

Generic Phylo

Defined in ELynx.Data.Tree.Phylogeny

Associated Types

type Rep Phylo :: Type -> Type

Methods

from :: Phylo -> Rep Phylo x

to :: Rep Phylo x -> Phylo

Semigroup Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

(<>) :: Phylo -> Phylo -> Phylo

sconcat :: NonEmpty Phylo -> Phylo

stimes :: Integral b => b -> Phylo -> Phylo

NFData Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

rnf :: Phylo -> ()

ToJSON Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

toJSON :: Phylo -> Value

toEncoding :: Phylo -> Encoding

toJSONList :: [Phylo] -> Value

toEncodingList :: [Phylo] -> Encoding

FromJSON Phylo

Defined in ELynx.Data.Tree.Phylogeny

Methods

parseJSON :: Value -> Parser Phylo

parseJSONList :: Value -> Parser [Phylo]

type Rep Phylo

Defined in ELynx.Data.Tree.Phylogeny

type Rep Phylo = D1 (MetaData "Phylo" "ELynx.Data.Tree.Phylogeny" "elynx-tree-0.3.2-D4z8hEm7d0IGPFAaza2gb3" False) (C1 (MetaCons "Phylo" PrefixI True) (S1 (MetaSel (Just "brLen") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe BranchLength)) :*: S1 (MetaSel (Just "brSup") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe BranchSupport))))

newtype Length

Branch length label.

For conversion, see phyloToLengthTree and lengthToPhyloTree.

Constructors

Length

Fields

• fromLength :: BranchLength

Instances

Eq Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

(==) :: Length -> Length -> Bool

(/=) :: Length -> Length -> Bool

Floating Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

pi :: Length

exp :: Length -> Length

log :: Length -> Length

sqrt :: Length -> Length

(**) :: Length -> Length -> Length

logBase :: Length -> Length -> Length

sin :: Length -> Length

cos :: Length -> Length

tan :: Length -> Length

asin :: Length -> Length

acos :: Length -> Length

atan :: Length -> Length

sinh :: Length -> Length

cosh :: Length -> Length

tanh :: Length -> Length

asinh :: Length -> Length

acosh :: Length -> Length

atanh :: Length -> Length

log1p :: Length -> Length

expm1 :: Length -> Length

log1pexp :: Length -> Length

log1mexp :: Length -> Length

Fractional Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

(/) :: Length -> Length -> Length

recip :: Length -> Length

fromRational :: Rational -> Length

Num Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

(+) :: Length -> Length -> Length

(-) :: Length -> Length -> Length

(*) :: Length -> Length -> Length

negate :: Length -> Length

abs :: Length -> Length

signum :: Length -> Length

fromInteger :: Integer -> Length

Ord Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

compare :: Length -> Length -> Ordering

(<) :: Length -> Length -> Bool

(<=) :: Length -> Length -> Bool

(>) :: Length -> Length -> Bool

(>=) :: Length -> Length -> Bool

max :: Length -> Length -> Length

min :: Length -> Length -> Length

Read Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

readsPrec :: Int -> ReadS Length

readList :: ReadS [Length]

readPrec :: ReadPrec Length

readListPrec :: ReadPrec [Length]

Show Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

showsPrec :: Int -> Length -> ShowS

show :: Length -> String

showList :: [Length] -> ShowS

Generic Length

Defined in ELynx.Data.Tree.Phylogeny

Associated Types

type Rep Length :: Type -> Type

Methods

from :: Length -> Rep Length x

to :: Rep Length x -> Length

Semigroup Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

(<>) :: Length -> Length -> Length

sconcat :: NonEmpty Length -> Length

stimes :: Integral b => b -> Length -> Length

Monoid Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

mempty :: Length

mappend :: Length -> Length -> Length

mconcat :: [Length] -> Length

NFData Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

rnf :: Length -> ()

ToJSON Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

toJSON :: Length -> Value

toEncoding :: Length -> Encoding

toJSONList :: [Length] -> Value

toEncodingList :: [Length] -> Encoding

FromJSON Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

parseJSON :: Value -> Parser Length

parseJSONList :: Value -> Parser [Length]

Measurable Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

getLen :: Length -> BranchLength

setLen :: BranchLength -> Length -> Length

Splittable Length

Defined in ELynx.Data.Tree.Phylogeny

Methods

split :: Length -> Length

type Rep Length

Defined in ELynx.Data.Tree.Phylogeny

type Rep Length = D1 (MetaData "Length" "ELynx.Data.Tree.Phylogeny" "elynx-tree-0.3.2-D4z8hEm7d0IGPFAaza2gb3" True) (C1 (MetaCons "Length" PrefixI True) (S1 (MetaSel (Just "fromLength") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BranchLength)))

phyloToLengthTree :: Tree Phylo a -> Either String (Tree Length a)

If root branch length is not available, set it to 0.

Return Left if any other branch length is unavailable.

lengthToPhyloTree :: Tree Length a -> Tree Phylo a

Set all branch support values to Nothing.

Useful, for example, to export a tree with branch lengths in Newick format.

newtype Support

Branch support label.

For conversion, see phyloToSupportTree.

Constructors

Support

Fields

• fromSupport :: BranchSupport

Instances

Eq Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

(==) :: Support -> Support -> Bool

(/=) :: Support -> Support -> Bool

Floating Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

pi :: Support

exp :: Support -> Support

log :: Support -> Support

sqrt :: Support -> Support

(**) :: Support -> Support -> Support

logBase :: Support -> Support -> Support

sin :: Support -> Support

cos :: Support -> Support

tan :: Support -> Support

asin :: Support -> Support

acos :: Support -> Support

atan :: Support -> Support

sinh :: Support -> Support

cosh :: Support -> Support

tanh :: Support -> Support

asinh :: Support -> Support

acosh :: Support -> Support

atanh :: Support -> Support

log1p :: Support -> Support

expm1 :: Support -> Support

log1pexp :: Support -> Support

log1mexp :: Support -> Support

Fractional Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

(/) :: Support -> Support -> Support

recip :: Support -> Support

fromRational :: Rational -> Support

Num Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

(+) :: Support -> Support -> Support

(-) :: Support -> Support -> Support

(*) :: Support -> Support -> Support

negate :: Support -> Support

abs :: Support -> Support

signum :: Support -> Support

fromInteger :: Integer -> Support

Ord Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

compare :: Support -> Support -> Ordering

(<) :: Support -> Support -> Bool

(<=) :: Support -> Support -> Bool

(>) :: Support -> Support -> Bool

(>=) :: Support -> Support -> Bool

max :: Support -> Support -> Support

min :: Support -> Support -> Support

Read Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

readsPrec :: Int -> ReadS Support

readList :: ReadS [Support]

readPrec :: ReadPrec Support

readListPrec :: ReadPrec [Support]

Show Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

showsPrec :: Int -> Support -> ShowS

show :: Support -> String

showList :: [Support] -> ShowS

Generic Support

Defined in ELynx.Data.Tree.Phylogeny

Associated Types

type Rep Support :: Type -> Type

Methods

from :: Support -> Rep Support x

to :: Rep Support x -> Support

Semigroup Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

(<>) :: Support -> Support -> Support

sconcat :: NonEmpty Support -> Support

stimes :: Integral b => b -> Support -> Support

NFData Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

rnf :: Support -> ()

ToJSON Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

toJSON :: Support -> Value

toEncoding :: Support -> Encoding

toJSONList :: [Support] -> Value

toEncodingList :: [Support] -> Encoding

FromJSON Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

parseJSON :: Value -> Parser Support

parseJSONList :: Value -> Parser [Support]

Splittable Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

split :: Support -> Support

Supported Support

Defined in ELynx.Data.Tree.Phylogeny

Methods

getSup :: Support -> BranchSupport

setSup :: BranchSupport -> Support -> Support

type Rep Support

Defined in ELynx.Data.Tree.Phylogeny

type Rep Support = D1 (MetaData "Support" "ELynx.Data.Tree.Phylogeny" "elynx-tree-0.3.2-D4z8hEm7d0IGPFAaza2gb3" True) (C1 (MetaCons "Support" PrefixI True) (S1 (MetaSel (Just "fromSupport") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BranchSupport)))

phyloToSupportTree :: Tree Phylo a -> Either String (Tree Support a)

Set branch support values of branches leading to the leaves and of the root branch to maximum support.

Return Left if any other branch has no available support value.

phyloToSupportTreeUnsafe :: Tree Phylo a -> Tree Support a

Set all unavailable branch support values to maximum support.

data PhyloStrict

Strict branch label for phylogenetic trees.

Constructors

PhyloStrict

Fields

• sBrLen :: BranchLength
• sBrSup :: BranchSupport

Instances

Eq PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

(==) :: PhyloStrict -> PhyloStrict -> Bool

(/=) :: PhyloStrict -> PhyloStrict -> Bool

Ord PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

compare :: PhyloStrict -> PhyloStrict -> Ordering

(<) :: PhyloStrict -> PhyloStrict -> Bool

(<=) :: PhyloStrict -> PhyloStrict -> Bool

(>) :: PhyloStrict -> PhyloStrict -> Bool

(>=) :: PhyloStrict -> PhyloStrict -> Bool

max :: PhyloStrict -> PhyloStrict -> PhyloStrict

min :: PhyloStrict -> PhyloStrict -> PhyloStrict

Read PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

readsPrec :: Int -> ReadS PhyloStrict

readList :: ReadS [PhyloStrict]

readPrec :: ReadPrec PhyloStrict

readListPrec :: ReadPrec [PhyloStrict]

Show PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

showsPrec :: Int -> PhyloStrict -> ShowS

show :: PhyloStrict -> String

showList :: [PhyloStrict] -> ShowS

Generic PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Associated Types

type Rep PhyloStrict :: Type -> Type

Methods

from :: PhyloStrict -> Rep PhyloStrict x

to :: Rep PhyloStrict x -> PhyloStrict

Semigroup PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

(<>) :: PhyloStrict -> PhyloStrict -> PhyloStrict

sconcat :: NonEmpty PhyloStrict -> PhyloStrict

stimes :: Integral b => b -> PhyloStrict -> PhyloStrict

ToJSON PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

toJSON :: PhyloStrict -> Value

toEncoding :: PhyloStrict -> Encoding

toJSONList :: [PhyloStrict] -> Value

toEncodingList :: [PhyloStrict] -> Encoding

FromJSON PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

parseJSON :: Value -> Parser PhyloStrict

parseJSONList :: Value -> Parser [PhyloStrict]

Measurable PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

getLen :: PhyloStrict -> BranchLength

setLen :: BranchLength -> PhyloStrict -> PhyloStrict

Splittable PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

split :: PhyloStrict -> PhyloStrict

Supported PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

Methods

getSup :: PhyloStrict -> BranchSupport

setSup :: BranchSupport -> PhyloStrict -> PhyloStrict

type Rep PhyloStrict

Defined in ELynx.Data.Tree.Phylogeny

type Rep PhyloStrict = D1 (MetaData "PhyloStrict" "ELynx.Data.Tree.Phylogeny" "elynx-tree-0.3.2-D4z8hEm7d0IGPFAaza2gb3" False) (C1 (MetaCons "PhyloStrict" PrefixI True) (S1 (MetaSel (Just "sBrLen") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BranchLength) :*: S1 (MetaSel (Just "sBrSup") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 BranchSupport)))

toStrictTree :: Tree Phylo a -> Either String (Tree PhyloStrict a)

Conversion to a PhyloStrict tree.

See phyloToLengthTree and phyloToSupportTree.

fromStrictTree :: Tree PhyloStrict a -> Tree Phylo a

Set all branch length and support values to Just the value.

Useful, for example, to export a tree with branch lengths in Newick format.