HI Gabriel,
There are THREE major differences between M8+BEB and MEME
1). MEME allows dS to vary from site to site. M8+BEB does not (see Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
for examples of how this can cause M8+BEB to confuse relaxation of constraint for positive selection).
2). M8+BEB is a random effects method, while MEME is a fixed effects method when it comes to estimating dS and dN at individual site. MEME will have more flexibility to fit the distribution of dS and dN (unlike M8+BEB which is limited to, say, beta + w)
3). Most critically, MEME can find episodes of selection (a burst of high omega values followed by negative selection), but M8+BEB can find only evidence of average selection (over branches). The MEME manuscript, where this is explained in detail, is currently in revision, but the following picture should clarify the difference.
Sergei