VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

Ali, Raja Hashim, 1985- (author): KTH,Beräkningsvetenskap och beräkningsteknik (CST),Lars Arvestad

Bark, Mikael (author): KTH,Skolan för informations- och kommunikationsteknik (ICT)

Miro, Jorge (author): KTH,Skolan för informations- och kommunikationsteknik (ICT)

Muhammad, Sayyed Auwn (author): KTH,Beräkningsvetenskap och beräkningsteknik (CST)

Zubair, Syed Muhammad (author): KTH,Kommunikationsnät,University of Balochistan, Pakistan

Abbas, Raja Manzar (author)

(creator_code:org_t)

Abstract Subject headings

Motivation: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical diculties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters.Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Availability: VMCMC is available for Java SE 6+ under the New BSD License. Executable jar les, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.

By the author/editor: Ali, Raja Hashim ...; Bark, Mikael; Miro, Jorge; Muhammad, Sayyed ...; Sjöstrand, Joel; Zubair, Syed Muh ...; show more...; Abbas, Raja Manz ...; Arvestad, Lars; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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