likelihood methods. It also provides several visualization tools for interpreting the results of ancestral reconstruction. MEGA is a modular system, too, but places greater emphasis on ease-of-use than customization of analyses. As of version 5, MEGA allows the user to reconstruct ancestral states using maximum parsimony, maximum likelihood, and empirical Bayes methods. The Bayesian analysis of genetic sequences may confer greater robustness to model misspecification. MrBayes allows inference of ancestral states at ancestral nodes using the full hierarchical Bayesian approach. The PREQUEL program distributed in the PHAST package performs comparative evolutionary genomics using ancestral sequence reconstruction. SIMMAP stochastically maps mutations on phylogenies. BayesTraits analyses discrete or continuous characters in a Bayesian framework to evaluate models of evolution, reconstruct ancestral states, and detect correlated evolution between pairs of traits. ProtASR performs ancestral sequence reconstruction (ASR) of proteins accounting for structural constraints. Other character types Other software packages are more oriented towards the analysis of qualitative and quantitative traits (phenotypes). For example, the ape package in the statistical computing environment R also provides methods for ancestral state reconstruction for both discrete and continuous characters through the 'ace' function, including maximum likelihood. Phyrex implements a maximum parsimony-based algorithm to reconstruct ancestral gene expression profiles, in addition to a maximum likelihood method for reconstructing ancestral genetic sequences (by wrapping around the baseml function in PAML). Several software packages also reconstruct phylogeography. BEAST (Bayesian Evolutionary Analysis by Sampling Trees) provides tools for reconstructing ancestral geographic locations from observed sequences annotated with location data using Bayesian MCMC sampling methods. Diversitree is an R package providing methods for ancestral state reconstruction under Mk2 (a continuous time Markov model of binary character evolution). and BiSSE (Binary State Speciation and Extinction) models. Lagrange performs analyses on reconstruction of geographic range evolution on phylogenetic trees. Phylomapper is a statistical framework for estimating historical patterns of gene flow and ancestral geographic locations. RASP infers ancestral states using statistical dispersal-vicariance analysis, Lagrange, Bayes-Lagrange, BayArea and BBM methods. VIP infers historical biogeography by examining disjunct geographic distributions. Genome rearrangements provide valuable information in comparative genomics between species. ANGES compares extant related genomes through ancestral reconstruction of genetic markers. BADGER uses a Bayesian approach to examining the history of gene rearrangement. Count reconstructs the evolution of the size of gene families. EREM analyses the gain and loss of genetic features encoded by binary characters. PARANA performs parsimony based inference of ancestral biological networks that