Trees: stop fighting!

Tree reconciliation in host-parasite coevolution or in gene-tree fitting has been a long-standing issue in evolutionary biology. Here's some programs that try to bring peace...

TreeMap: for cophylogeny mapping.

TreeFitter: for MP tree-fitting.

SoftParsMap: maps gene trees onto species trees using soft parsimony.

gtp: species tree reconciliation and gene tree parsimony.

UREC: for computing unrooted gene and rooted species tree reconciliation.

CopyCat: easy & fast access to co-phylogenetic analyses. has a wrapper for ParaFit that tests for the association of host and parasite phylogenies.

PriMETV: visualizes tree-within-tree phenomena.