--- name: "tree-ppuzzle" section: "1" platform: "linux" package: "tree-ppuzzle" version: "5.3~rc16+dfsg-12+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/tree-ppuzzle" --- # tree-ppuzzle(1) Reconstruction of phylogenetic trees by maximum likelihood (parallelized version) ## NAME tree-ppuzzle - Reconstruction of phylogenetic trees by maximum likelihood (parallelized version) ## SYNOPSIS **tree-ppuzzle** ## DESCRIPTION This manual page documents briefly the **tree-ppuzzle** command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. TREE-PPUZZLE is the new name for the program previously known as PPUZZLE! **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-PPUZZLE 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-PPUZZLE 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. This program is the paralelized version of tree-puzzle. ## 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-puzzle**(1)](/tree-puzzle/1.md). This manual page was written by Dr. Guenter Bechly \, for the Debian GNU/Linux system (but may be used by others).