BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

AJ Drummond, 2007, Beast: Bayesian evolutionary analysis by sampling trees, BMC Evol Biol, 7, 214, 10.1186/1471-2148-7-214

AJ Drummond, 2012, Bayesian phylogenetics with beauti and the beast 1.7, Mol Biol Evol, 29, 1969, 10.1093/molbev/mss075

AJ Drummond, 2006, Relaxed phylogenetics and dating with confidence, PLoS Biol, 4, e88, 10.1371/journal.pbio.0040088

AJ Drummond, 2005, Bayesian coalescent inference of past population dynamics from molecular sequences, Mol Biol Evol, 22, 1185, 10.1093/molbev/msi103

V Minin, 2008, Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics, Molecular Biology and Evolution, 25, 1459, 10.1093/molbev/msn090

J Heled, 2010, Bayesian inference of species trees from multilocus data, Mol Biol Evol, 27, 570, 10.1093/molbev/msp274

P Lemey, 2009, Bayesian phylogeography finds its roots, PLoS Comput Biol, 5, e1000520, 10.1371/journal.pcbi.1000520

P Lemey, 2010, Phylogeography takes a relaxed random walk in continuous space and time, Mol Biol Evol, 27, 1877, 10.1093/molbev/msq067

RR Bouckaert, 2010, Densitree: making sense of sets of phylogenetic trees, Bioinformatics, 26, 1372, 10.1093/bioinformatics/btq110

M Suchard, 2009, Many-core algorithms for statistical phylogenetics, Bioinformatics, 25, 1370, 10.1093/bioinformatics/btp244

D Ayres, 2012, Beagle: a common application programming inferface and high-performance computing library for statistical phylogenetics, Syst Biol, 61, 170, 10.1093/sysbio/syr100

G Baele, 2012, Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty, Molecular Biology and Evolution

A Alekseyenko, 2008, Wagner and Dollo: a stochastic duet by composing two parsimonious solos, Systematic Biology, 57, 772, 10.1080/10635150802434394

J Heled, 2008, Bayesian inference of population size history from multiple loci, BMC Evolutionary Biology, 8, 289, 10.1186/1471-2148-8-289

L Kuo, 1998, Variable selection for regression models, Sankhya: The Indian Journal of Statistics, Series B (1960–2002), 60, 65

CH Wu, 2013, Bayesian selection of nucleotide substitution models and their site assignments, Mol Biol Evol, 30, 669, 10.1093/molbev/mss258

M Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of molecular evolution, 16, 111, 10.1007/BF01731581

J Felsenstein, 1981, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, 17, 368, 10.1007/BF01734359

M Hasegawa, 1985, Dating of the human-ape splitting by a molecular clock of mitochondrial dna, Journal of molecular evolution, 22, 160, 10.1007/BF02101694

K Tamura, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial dna in humans and chimpanzees, Molecular Biology and Evolution, 10, 512

S Tavaré, 1986, Some probabilistic and statistical problems in the analysis of dna sequences, Lect Math Life Sci, 17, 57

K Hayasaka, 1988, Molecular phylogeny and evolution of primate mitochondrial dna, Mol Biol Evol, 5, 626

T Stadler, 2013, Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and HCV, PNAS, 110, 228, 10.1073/pnas.1207965110

Kühnert D. Phylodynamics package. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://phylodynamics.googlecode.com" xlink:type="simple">http://phylodynamics.googlecode.com</ext-link>. Accessed: 2014-01-31.

D Kühnert, 2014, Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death sir model, J R Soc Interface, 11, 10.1098/rsif.2013.1106

Vaughan T. Multitypetree package. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/CompEvol/MultiTypeTree" xlink:type="simple">https://github.com/CompEvol/MultiTypeTree</ext-link>. Accessed: 2014-01-31.

T Vaughan, 2013, Efficient sampling of multi-type trees for bayesian phylogenetic inference

P Beerli, 1999, Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach, Genetics, 152, 763, 10.1093/genetics/152.2.763

P Beerli, 2001, Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach, Proc Natl Acad Sci U S A, 98, 4563, 10.1073/pnas.081068098

P Beerli, 2006, Comparison of bayesian and maximum-likelihood inference of population genetic parameters, Bioinformatics, 22, 341, 10.1093/bioinformatics/bti803

T van de Laar, 2009, Evidence of a large, international network of HCV transmission in HIV-positive men who have sex with men, Gastroenterology, 136, 1609, 10.1053/j.gastro.2009.02.006

R Bouckaert, 2013, Evolutionary rates and hbv: issues of rate estimation with bayesian molecular methods, Antiviral therapy, 18, 497, 10.3851/IMP2656

D Bryant, 2012, Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis, Mol Biol Evol, 29, 1917, 10.1093/molbev/mss086

T Vaughan, 2013, A stochastic simulator of birth-death master equations with application to phylodynamics, Mol Biol Evol, 30, 1480, 10.1093/molbev/mst057