For efficiently handling thousands of malware specimens, we aim to quickly and automatically categorize those into malware families. A solution for this could be the neighbor-joining method using NCD (Normalized Compression Distance) as similarity of malware. It creates a phylogenetic tree of malware based on the NCDs between malware binaries for clustering. However, it is frustratingly slow because it requires \((N^2+N)/2\) compression attempts for the NCDs, where N is the number of given specimens. For fast clustering, this paper presents an algorithm for efficiently constructing a phylogenetic tree by greatly reducing compression attempts. The key idea to do so is not to construct a tree of N specimens all at once. Instead, it divides N specimens into temporal clusters in advance, constructs a small tree for each temporal cluster, and joins the trees as a united tree. Intuitively, separately constructing small trees requires a much smaller number of compression attempts than \((N^2+N)/2\). With experiments using 4,109 in-the-wild malware specimens, we confirm that our algorithm achieved clustering 22 times faster than the neighbor-joining method with a good accuracy of 97%.