Getting started with ACG
Importing dataTo be able to use your sequence data in ACG you must first 'import' it. There are two ways to do this. First, if you have a .fasta formatted alignment, just click the button in the upper left corner of the screen, then select your file. Alternatively, if you have a .VCF formatted file from your latest NGS experiment, click the next button over. You'll be asked to supply a reference file and a sub-region to import. After you import some data, it will appear in a folder on the left side of the screen. Double click it to see the data and begin the analysis.
Creating an analysisEach analysis in ACG can involve many parameters, priors, proposal kernels, and loggers. To make life a bit simpler ACG provides four default analysis types (Quick, Basic, Demographic, and Thorough) with some sensible choices (you can always change the settings later). Decide which option is best for you, then click the "Choose" button at the bottom right.
Fine-tuning the settings
Once you've chosen a basic analysis type, you can further refine your settings. You can choose to have different types of data collected by modifying the "loggers", each of which collects different kinds of data about your run - for instance, the shapes of the trees ancestral to a site, or the location of recombination breakpoints. In addition to the loggers, you can modify the settings for every (well, almost every) parameter - its name, its prior type, the range of allowable values, etc.
Running the model
When you're done fiddling with the settings, click the big green "Begin" button to start the analysis. ACG will begin running the analysis - but, since it ignores the first portion of all MCMC states, not much data may appear right away. After a minute or two the chain will leave the "burn-in" state and you can start to visualize the results. You can save images of the figures, export the raw data (in .csv format), or configure fonts, colors, and limits by clicking the buttons at the bottom of each tab.
Handling multiple analyses
If you create and run an analysis while another is already running, the second analysis will wait to run until the first completes. This way it's easy to "submit" many jobs and have them all run overnight, or over the weekend. By clicking on the "Job List" button (the far right button on the small toolbar at the top-left of the screen) you can view and modify all the scheduled jobs.