The structure of Markov equivalence classes (MECs) of causal DAGs has been studied extensively. A natural question in this regard is to algorithmically find the number of MECs with a given skeleton. Until recently, the known results for this problem were in the setting of very special graphs (such as paths, cycles, and star graphs). More recently, a fixed-parameter tractable (FPT) algorithm was given for this problem which, given an input graph $G$, counts the number of MECs with the skeleton $G$ in $O(n(2^{O(d^4k^4)} + n^2))$ time, where $n$, $d$, and $k$, respectively, are the numbers of nodes, the degree, and the treewidth of $G$. We give a faster FPT algorithm that solves the problem in $O(n(2^{O(d^2k^2)} + n^2))$ time when the input graph is chordal. Additionally, we show that the runtime can be further improved to polynomial time when the input graph $G$ is a tree.

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