{"added":null,"apiVersion":1,"behindSince":null,"buildDepends":[],"categories":["biology"],"comment":"Maximum likelihood analysis of molecular sequence data","compare":null,"dependentCount":null,"description":"PUZZLE is a computer program to reconstruct phylogenetic trees\nfrom molecular sequence data by maximum likelihood.  It implements\na fast tree search algorithm, quartet puzzling, that allows\nanalysis of large data sets and automatically assigns estimations\nof support to each internal branch.  PUZZLE also computes pairwise\nmaximum likelihood distances as well as branch lengths for user\nspecified trees.  Branch lengths can also be calculated under the\nclock-assumption.  In addition, PUZZLE offers a novel method,\nlikelihood mapping, to investigate the support of a hypothesized\ninternal branch without computing an overall tree and to\nvisualize the phylogenetic content of a sequence alignment.\nPUZZLE also conducts a number of statistical tests on the data\nset (chi-square test for homogeneity of base composition,\nlikelihood ratio to test the clock hypothesis, Kishino-Hasegaw a\ntest).  The models of substitution provided by PUZZLE are TN, HKY,\nF84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for\namino acids, and F81 for two-state data.  Rate heterogeneity is\nmodelled by a discrete Gamma distribution and by allowing\ninvariable sites.  The corresponding parameters can be inferred\nfrom the data set.","flavors":[],"html":"https://daemonports.org/netbsd/biology/puzzle/","kind":"port","lastUpdate":null,"license":["gnu-gpl-v2"],"maintainer":"babafou@babafou.eu.org","name":"puzzle","newest":false,"newestVersion":null,"noVulnData":false,"origin":"biology/puzzle","otherSystems":[],"packages":[{"repo":"NetBSD 10.1 x86_64","versions":["5.2nb2"]},{"repo":"NetBSD 10.1 aarch64","versions":["5.2nb2"]},{"repo":"SmartOS / illumos x86_64","versions":["5.2nb2"]},{"repo":"macOS 15 arm64","versions":["-"]}],"pkgName":"puzzle-5.2nb2","related":null,"repository":"pkgsrc","requiredBy":[],"requiredByCount":0,"runDepends":["parallel/mpi-ch"],"status":null,"system":"netbsd","systemLabel":"NetBSD","version":"5.2nb2","versions":null,"vulnerabilities":null,"www":"http://www.tree-puzzle.de/"}