TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It 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 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. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.
v5.2 :: 0 :: gentoo
- x86 ~amd64 ~amd64-linux ~ppc ~ppc-macos ~x86-linux
- USE flags
- Add MPI (Message Passing Interface) layer to the apps that support it
- sci-biology/tree-puzzle-5.2 : ./ppuzzle.c:300:2: error: static assertion failed: MPI_Address was removed in MPI-3.0. Use MPI_Get_address instead.
- Repository mirror & CI · gentoo
Merge updates from master
- David Seifert · gentoo
sci-biology/tree-puzzle: Port to EAPI 7
Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <email@example.com>
- Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <firstname.lastname@example.org>
- Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <email@example.com> X-Thanks: Alec Warner <firstname.lastname@example.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <email@example.com> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <firstname.lastname@example.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <email@example.com> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <firstname.lastname@example.org> - validation scripts X-Thanks: Patrick Lauer <email@example.com> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <firstname.lastname@example.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed