Crate light_phylogeny[−][src]
Expand description
light structures and functions for phylogeny
light_phylogeny
is a set of structures and functions dedicated to reading, building,
manipulating and displaying phylogenic trees, especially reconciled trees with speciation,
duplication, loss and horizontal transfer events. Read newick, phyloXML and recPhyloXML files.
Structs
Structure ArenaTree.
Structure Config: drawing config.
Structure Noeud.
Structure Options: drawing options.
Enums
enum of the possible events in a gene tree
Functions
Add a node to another node
Check if tree in newick format is rooted
Draw a svg pipe species tree and several gene trees inside it
Draw a svg simple tree
Get the transfers in a gene tree
Send the index of the last common ancestor of 2 nodes
Map gene trees to host tree
Map a reconciled species tree to a pipe species tree
Map a pipe species tree to a reconciled species tree
Map a transfert in gene tree to the species tree
Move a node from a parent node to another node
Fill an ArenaTree structure with the contents of a parentheses tree.
Create a svg of the tree in phyloxml context
Read a newick file and store the tree into ArenaTree structure
Read a phyloxml file and store the tree into a ArenaTree structure
Read a recphyloxml file and store the species and gene trees into several ArenaTree structures
Transforms the tree into real branch length representation
Create a svg of the tree in recphyloxml context
Reset all positions x y xmod ymod of the tree
Scaling tree height
Scaling width height
Display a short summary of each node of the tree