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

BMC Bioinformatics

Software

Raja M. Abbas¹  Lars Arvestad²  Joel Sjöstrand²  Syed M. Zubair³  Mikael Bark⁴  Jorge Miró⁴  Sayyed A. Muhammad⁵  Raja H. Ali⁵ 

[1] Department of Computer Science and Engineering, University of Gothenburg, SE-411 37, Gothenburg, Sweden;Department of Numerical Analysis and Computer Science, Swedish e-Science Research Centre, Science for Life Laboratory, Stockholm University, SE-100 44, Stockholm, Sweden;KTH Royal Institute of Technology, Laboratory for Communication Networks, School of Electrical Engineering, SE-100 44, Stockholm, Sweden;Department of Computer Science and Information Technology, University of Balochistan, PK-87 300, Quetta, Pakistan;KTH Royal Institute of Technology, School of Information and Communication Technology, SE-164 40, Kista, Sweden;KTH Royal Institute of Technology, Swedish e-Science Research Centre, Science for Life Laboratory, School of Computer Science and Communication, SE-171 77, Solna, Sweden;

关键词: Convergence;    Markov chain Monte Carlo;    Metropolis-Hastings;    Phylogenetics;    Software;    Visualization;   

DOI  :  10.1186/s12859-017-1505-3

 received in 2015-11-07, accepted in 2017-01-28,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMCMC-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 difficulties 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.ResultsWe 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.ConclusionsVMCMC is a free software available under the New BSD License. Executable jar files, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.

【 授权许可】

CC BY   
© The Author(s) 2017