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
ArenaTree | Structure ArenaTree. |
Config | Structure Config: drawing config. |
Noeud | Structure Noeud. |
Options | Structure Options: drawing options. |
Enums
Event | enum of the possible events in a gene tree |
Functions
add_child | Add a node to another node |
check_is_rooted | Check if tree in newick format is rooted |
draw_sptree_gntrees | Draw a svg pipe species tree and several gene trees inside it |
draw_tree | Draw a svg simple tree |
get_gtransfer | Get the transfers in a gene tree |
lca | Send the index of the last common ancestor of 2 nodes |
map_parasite_g2s | Map a reconciled species tree to a pipe species tree |
map_parasite_s2g | Map a pipe species tree to a reconciled species tree |
map_transfer | Map a transfert in gene tree to the species tree |
map_transfer_mul | |
move_child | Move a node from a parent node to another node |
newick2tree | Fill an ArenaTree structure with the contents of a parentheses tree. |
phyloxml_processing | Create a svg of the tree in phyloxml context |
read_newick | Read a newick file and store the tree into ArenaTree structure |
read_phyloxml | Read a phyloxml file and store the tree into a ArenaTree structure |
read_recphyloxml | Read a recphyloxml file and store the species and gene trees into several ArenaTree structures |
read_recphyloxml_multi | Read a recphyloxml file and store the species and gene trees into several ArenaTree structures |
real_length | Transforms the tree into real branch length representation |
recphyloxml_processing | Create a svg of the tree in recphyloxml context |
reset_pos | Reset all positions x y xmod ymod of the tree |
scale_heigth | Scaling tree height |
scale_width | Scaling width height |
summary | Display a short summary of each node of the tree |