Bioinformatics: VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces
Analysing the output from Markov chain Monte Carlo (MCMC) computations is a crucial step in many scientific investigations today, and in particular in evolutionary studies where MCMC has proved to be a strong and flexible framework. VMCMC is a convenient tool with two aims: to make phylogenetic MCMC trace analysis of multiple experiments convenient, especially in a HPC environment, and to simplify visualisation of single traces.
MCMC traces are often analysed using R, but we have needed a dedicated tool that enables easier and faster analysis for the use cases that have been important to us. Output from applications in our JPrIME package is a particular concern, but the ambition has been to provide a tool that can handle output from other software (such as MrBayes, RevBayes, BEAST) as well.
A paper on VMCMC was published in BMC Bioinformatics early this year, summarising and explaining the main features.