--- name: "tree-puzzle" section: "1" platform: "linux" package: "tree-puzzle" version: "5.3~rc16+dfsg-12+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/tree-puzzle" --- # tree-puzzle(1) Reconstruction of phylogenetic trees by maximum likelihood ## NAME tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood ## SYNOPSIS **tree-puzzle** ## DESCRIPTION This manual page documents briefly the **tree-puzzle** command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. TREE-PUZZLE is the new name for the program previously known as PUZZLE! **tree-puzzle** is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. There is also a paralellized version tree-ppuzzle available. ## OPTIONS There are no options. For usage please look at /usr/share/doc/tree-puzzle/tree-puzzle.pdf. ## SEE ALSO [**phylip**(1)](/phylip/1.md), **treetool**(1). [**tree-ppuzzle**(1)](/tree-ppuzzle/1.md). This manual page was written by Dr. Guenter Bechly \, for the Debian GNU/Linux system (but may be used by others).