# đī¸ nwk2phy is a fast converter from Newick trees to Phylip distance matrices Typical computation of distance between leaves in a tree takes $O(n)$ time. Hence, computing pairwise distance between leaves of the tree would take $O(n^3)$ time. While polynomial, it becomes already impractical for moderate collections (eg. 1000 genomes). The `nwk2phy` relies on the folklore construction of datastructure able to answer Lowest Common Ancestor in the tree in constant time. This comes at the price of extra linear space, build during a linear time preprocessing phase. Afterward, the distance queries can be answered in $O(1)$ time, leading to an (asymptotically) optimal complexity of $O(n^2)$. **Note.** This program uses an advanced approach, supplying its speed, but is no further optimized. ## đĨī¸ Usage ``` text â ââ â ââââââââââââŖâââ ââââģââââââŖâââââĢ v.0.1 â â A simple converter from Newick trees to Phylip distance matrices in O(n^2) time Copyright (c) LÊo Ackermann 2024 USAGE nwk2phy -h/--help âš Display this message nwk2phy <newick file> --out=<outfile> [--ord=<order>] âš Convert the input Newick file into a Phylip distance matrix <order> is the order of the matrix rows, the leftmost being the smallest with respect to the order LEAVES is the left-to-right leaves order of the tree (default) LEXICO is the lexicographic order ```