Tree simulations and randomizations
[This page is under construction]
Various packages in Mesquite can simulate or randomize trees,
allowing you to build statistical tests based on null distributions
or trees generated under some hypothesis. Trees so generated can
be used directly in charts and the tree window (selecting, for
example, Simulate Tree as a tree source), or they can be stored
in tree blocks using the "Make New Trees Block From"
submenu of the Taxa&Trees menu.
Evolutionary Simulations of Trees
- Uniform speciation (Yule) (trees package)
— Generates tree by simple uniform probability speciation (a
Yule process) as done by Harding, 1971. The chance of speciation
is equal for all tips. Options: total time depth of tree.
- Coalescent Trees (coalesce package) — Generates
tree by coalescence within a single panmictic population. Options:
Effective population size.
- Coalescence Contained within Current Tree
(coalesce package) — Generates tree by a simple coalescence
model of a neutral gene with constant population size, within
a current species tree from a Tree window or other tree context.
Branch lengths are assigned according to generation of coalescence.
The species tree used is a current tree found in a Tree Window
or other tree context.
- Equiprobable Trees (trees package)— Generates
trees randomly so that each possible labelled tree topology
is equally likely.
- Randomly Resolve Polytomies (TreeFarm package)
— Randomly resolves polytomies in tree. All possible resolutions
are equiprobable. Thus, if the tree is a polytomous bush, the
resulting resolved trees will be distributed equivalently to
that from the Equiprobable Trees module.
- Reshuffle Terminal Taxa (TreeFarm package)
— Shuffles (permutes) the taxa among the terminal nodes.
- Add Noise to Branch Lengths (TreeFarm package)
— Adds noise to branch lengths of tree. Noise is Normally distributed
and proportional to current branch length, except that negative
branch lengths are not allowed; changed to zero. Options: variance
- Add Noise to Divergence Times (TreeFarm package)
— Adds noise to branch positions, i.e. divergence times in tree.
Noise is Normally distributed and proportional to current branch
lengths, except that negative branch lengths are not allowed;
changed to zero. Options: variance of noise.
- Rarefy Tree (TreeFarm package) — Rarefies
tree by randomly deleting taxa. Options: how many excluded.
- Augment Tree Randomly (TreeFarm package)
— Augments tree by random placement of excluded taxa. Options:
whether branch lengths are to be considered; whether addition
is only to original branches
2002-2003 by Wayne P. Maddison and David R. Maddison.
All rights reserved.