{"added":null,"apiVersion":1,"behindSince":null,"buildDepends":[],"categories":["biology"],"comment":"Maximum likelihood phylogeny reconstruction using quartets","compare":null,"dependentCount":null,"description":"TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from\nmolecular sequence data by maximum likelihood. It implements a fast tree search\nalgorithm, quartet puzzling, that allows analysis of large data sets and\nautomatically assigns estimations of support to each internal branch.\nTREE-PUZZLE also computes pairwise maximum likelihood distances as well as\nbranch lengths for user specified trees. Branch lengths can be calculated under\nthe clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood\nmapping, to investigate the support of a hypothesized internal branch without\ncomputing an overall tree and to visualize the phylogenetic content of a\nsequence alignment. TREE-PUZZLE also conducts a number of statistical tests on\nthe data set (chi-square test for homogeneity of base composition, likelihood\nratio clock test, Kishino-Hasegawa test). The models of substitution provided by\nTREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT,\nWAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity\nis modeled by a discrete Gamma distribution and by allowing invariable sites.\nThe corresponding parameters can be inferred from the data set.","flavors":[],"html":"https://daemonports.org/dragonfly/biology/treepuzzle/","kind":"port","lastUpdate":null,"license":null,"maintainer":"jan.lentfer@web.de","name":"treepuzzle","newest":true,"newestVersion":"5.2","noVulnData":false,"origin":"biology/treepuzzle","otherSystems":[{"maintainer":"jan.lentfer@web.de","newest":true,"origin":"biology/treepuzzle","path":"/biology/treepuzzle/","system":"FreeBSD","version":"5.2"},{"maintainer":"jan.lentfer@web.de","newest":true,"noVulnData":true,"origin":"biology/treepuzzle","path":"","system":"HardenedBSD","version":"5.2"},{"maintainer":"jan.lentfer@web.de","newest":true,"noVulnData":true,"origin":"biology/treepuzzle","path":"","system":"GhostBSD","version":"5.2"}],"packages":null,"pkgName":"treepuzzle-5.2","related":null,"repository":"DPorts","requiredBy":[],"requiredByCount":0,"runDepends":[],"status":null,"system":"dragonfly","systemLabel":"DragonFly","version":"5.2","versions":null,"vulnerabilities":null,"www":"http://www.tree-puzzle.de"}