Ancestral Reconstruction

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

(2015) Yan Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution

(2014) Michael G Elliot et al.   BMC EVOLUTIONARY BIOLOGY

An Evaluation of Phylogenetic Methods for Reconstructing Transmitted HIV Variants using Longitudinal Clonal HIV Sequence Data

(2014) R. M. McCloskey et al.   JOURNAL OF VIROLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Phylogenetic Quantification of Intra-tumour Heterogeneity

(2014) Roland F. Schwarz et al.   PLoS Computational Biology

The Phylogeny of Little Red Riding Hood

(2013) Jamshid J. Tehrani   PLoS One

Parsimonious reconstruction of network evolution

(2012) Rob Patro et al.   Algorithms for Molecular Biology

ANGES: reconstructing ANcestral GEnomeS maps

(2012) B. R. Jones et al.   BIOINFORMATICS

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

(2012) Graham J. Slater et al.   EVOLUTION

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Evolutionary inference via the Poisson Indel Process

(2012) Alexandre Bouchard-Côté et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

(2012) Art F. Y. Poon et al.   PLoS Computational Biology

Spatial analysis of vicariance: a method for using direct geographical information in historical biogeography

(2011) J. Salvador Arias et al.   CLADISTICS

Evolutionary History of Hunter-Gatherer Marriage Practices

(2011) Robert S. Walker et al.   PLoS One

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

(2010) Victor Hanson-Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fossils provide better estimates of ancestral body size than do extant taxa in fishes

(2009) James S. Albert et al.   ACTA ZOOLOGICA

Ancestors 1.0: a web server for ancestral sequence reconstruction

(2009) A. B. Diallo et al.   BIOINFORMATICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites

(2008) N. Gruenheit et al.   MOLECULAR BIOLOGY AND EVOLUTION

More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States

(2008) Guoliang Li et al.   SYSTEMATIC BIOLOGY

A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages

(2008) John R. Clark et al.   SYSTEMATIC BIOLOGY

A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape

(2008) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY