package phylogenetics

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Algorithms and datastructures for phylogenetics

Install 

dune-project
 Dependency

github.com Readme Edit opam file Versions (4)

Authors

  1. L
    Louis Duchemin
  2. V
    Vincent Lanore
  3. P
    Philippe Veber

Maintainers

  1. P
    philippe.veber@gmail.com

Sources

phylogenetics-0.3.0.tbz
sha256=de867d7cc017a8e434dab43ef16f0f6495973892cd7b6a8446b18e79393704a8
sha512=0209538caf94be47eabcaa25399c54849bd4fa0fc79e0579acee27f46ef3b72aa50e17bdb48fed8e86674d4caee6c1c4c423833a2757db12e2a6cc28234510de

doc/phylogenetics/Phylogenetics/Tree/index.html

Module Phylogenetics.TreeSource

Tree structure with annotations on leaves, internal nodes and branches.

Sourcetype ('n, 'l, 'b) t =
  1. | Node of {
    1. data : 'n;
    2. branches : ('n, 'l, 'b) branch List1.t;
    }
  2. | Leaf of 'l

Node { data; branches } represents a node in the tree with node data of type 'n and a non-empty list of branches

Leaf l represents a leaf in the tree with leaf data of type 'l.

Sourceand ('n, 'l, 'b) branch =
  1. | Branch of {
    1. data : 'b;
    2. tip : ('n, 'l, 'b) t;
    }
Sourceval sexp_of_t : ('n -> Sexplib0.Sexp.t) -> ('l -> Sexplib0.Sexp.t) -> ('b -> Sexplib0.Sexp.t) -> ('n, 'l, 'b) t -> Sexplib0.Sexp.t
Sourceval sexp_of_branch : ('n -> Sexplib0.Sexp.t) -> ('l -> Sexplib0.Sexp.t) -> ('b -> Sexplib0.Sexp.t) -> ('n, 'l, 'b) branch -> Sexplib0.Sexp.t
Sourceval t_of_sexp : (Sexplib0.Sexp.t -> 'n) -> (Sexplib0.Sexp.t -> 'l) -> (Sexplib0.Sexp.t -> 'b) -> Sexplib0.Sexp.t -> ('n, 'l, 'b) t
Sourceval branch_of_sexp : (Sexplib0.Sexp.t -> 'n) -> (Sexplib0.Sexp.t -> 'l) -> (Sexplib0.Sexp.t -> 'b) -> Sexplib0.Sexp.t -> ('n, 'l, 'b) branch
Sourceval leaf : 'l -> (_, 'l, 'b) t

leaf l constructs a leaf node with data l.

Sourceval node : 'a -> ('a, 'b, 'c) branch List1.t -> ('a, 'b, 'c) t

node a branches constructs a node with data a and the given list of branches.

Sourceval binary_node : 'a -> ('a, 'b, 'c) branch -> ('a, 'b, 'c) branch -> ('a, 'b, 'c) t

binary_node a b1 b2 constructs a binary node with data a and the two branches b1 and b2.

Sourceval branch : 'c -> ('a, 'b, 'c) t -> ('a, 'b, 'c) branch

branch c tip constructs a branch with data c and the given sub-tree tip.

Sourceval data : ('a, 'a, _) t -> 'a

data t returns the data contained in the leaf or root node of the tree t.

Sourceval to_printbox : ?node:('n -> string) -> ?leaf:('l -> string) -> ?branch:('b -> string option) -> ('n, 'l, 'b) t -> PrintBox.t

to_printbox ?node ?leaf ?branch t converts the tree t to a printable representation using the provided functions for converting node, leaf, and branch data to strings.

Sourceval map : ('a, 'b, 'c) t -> node:('a -> 'd) -> leaf:('b -> 'e) -> branch:('c -> 'f) -> ('d, 'e, 'f) t

map t ~node ~leaf ~branch maps the node, leaf, and branch data of the tree t using the provided functions node, leaf, and branch, respectively.

Sourceval map_branches : ('a, 'b, 'c) t -> node:('a -> 'd) -> leaf:('b -> 'd) -> branch:('d -> 'c -> 'd -> 'e) -> ('a, 'b, 'e) t
Sourceval map2_exn : ('a, 'b, 'c) t -> ('d, 'e, 'f) t -> node:('a -> 'd -> 'x) -> leaf:('b -> 'e -> 'y) -> branch:('c -> 'f -> 'z) -> ('x, 'y, 'z) t

map2_exn t1 t2 ~node ~leaf ~branch maps the corresponding node, leaf, and branch data of the trees t1 and t2 using functions node, leaf, and branch, respectively. Raises an exception if the two trees have different structures.

Sourceval map_branch2_exn : ('a, 'b, 'c) branch -> ('d, 'e, 'f) branch -> node:('a -> 'd -> 'x) -> leaf:('b -> 'e -> 'y) -> branch:('c -> 'f -> 'z) -> ('x, 'y, 'z) branch

map_branch2_exn b1 b2 ~node ~leaf ~branch maps the corresponding node, leaf, and branch data of the branches b1 and b2 using functions node, leaf, and branch, respectively. Raises an exception if the two branches have different structures.

Sourceval propagate : ('n1, 'l1, 'b1) t -> init:'s -> node:('s -> 'n1 -> 's * 'n2) -> leaf:('s -> 'l1 -> 'l2) -> branch:('s -> 'b1 -> 's * 'b2) -> ('n2, 'l2, 'b2) t

propagate t ~init ~node ~leaf ~branch propagates the values of node, leaf, and branch data in the tree t using the provided update functions node, leaf, and branch. The initial state init is threaded through the propagation.

Sourceval prefix_traversal : ('n, 'l, 'b) t -> init:'c -> node:('c -> 'n -> 'c) -> leaf:('c -> 'l -> 'c) -> branch:('c -> 'b -> 'c) -> 'c

prefix_traversal t ~init ~node ~leaf ~branch performs a prefix traversal of the tree t using the provided update functions node, leaf, and branch. The initial state init is threaded through the traversal. Returns the final state after the traversal.

Sourceval leaves : (_, 'l, _) t -> 'l list

leaves t returns a list of all leaf data in the tree t.

Sourceval fold_leaves : (_, 'l, _) t -> init:'a -> f:('a -> 'l -> 'a) -> 'a

fold_leaves t ~init ~f folds over the leaf data in the tree t using the provided folding function f and initial accumulator init. Returns the final accumulator after folding.

Sourceval unfold : ('n, 'l, 'b) t -> init:'a -> branch:('e -> 'b -> 'a * 'bb) -> leaf:('a -> 'l -> 'e * 'll) -> node:('a -> 'n -> 'e * 'nn) -> ('nn, 'll, 'bb) t

unfold t ~init ~branch ~leaf ~node unfolds the tree t into a new tree using the provided functions branch, leaf, and node. The initial state init is threaded through the unfolding.

Sourceval leafset_generated_subtree : ('n, 'l, 'b) t -> ('l -> string option) -> string list -> ('n, 'l, 'b) t option

leafset_generated_subtree t f xs returns the maximal subtree of t whose leaves all return a string in xs when applied to f if it exists (and None otherwise)

Sourceval simplify_node_with_single_child : merge_branch_data:('b list -> 'b) -> ('n, 'l, 'b) t -> ('n, 'l, 'b) t

simplify_node_with_single_child ~merge_branch_data t simplifies the tree t by merging nodes with a single child using the provided merging function merge_branch_data.