#### Miscellaneous 2

**PhyNav (Phylogenetic Navigator)**

A tree sampling method to reconstruct phylogenetic trees
from really large datasets (DNA and protein).
The method combines different methods to sample good trees.
PhyNav homepage.

**(p)IPHULA [(parallel) Inference of Population History Using a Likelihood Approach]**

(p)IPHULA is a software that investigates parameters of
population history based on a Monte Carlo simulation using
the maximum likelihood framework.
IPHULA/pIPHULA homepage.

**PluMiST - Plus and Minus SuperTrees**

PluMiST is a computer program to reconstruct and evaluate
majority rule supertrees: MR(-), MR(+) and MR(+)g.
The software is available at the
PluMiST homepage.

**SIMULATOR**

Software to simulate DNA and protein datasets with well-defined
insertion-deletion dynamics according to a user-given tree.
The software is available at the
SIMULATOR homepage.

**Shortest Triplet Clustering (STC)**

A new distance-based clustering method to reconstruct
very large phylogenies in polynomial time O(n^2) for n sequences.
The package is available at the
STC homepage.

**MRC.py**

is a computer program to evaluate the compatibility lengths given supertrees and gene trees and to extract the supertrees with the minimal lengths.
The program is available at the
MRC homepage.

**GenerateTrees**

is a program to generate all or a random set of trees for a given set of taxon names.
The package is available at the
GenerateTrees homepage

**Parat**

estimates site specific substitution rates from a set of DNA sequences.
The package is available at the
Parat homepage.