:: DESCRIPTION
ParaTree is a parametric tool for aligning two ordered trees. There are two versoins depending on whether gap penalty is considered.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2003 Nov 22;19(17):2237-45.
Parametric alignment of ordered trees.
Wang L, Zhao J.
:: DESCRIPTION
Given a (dated) species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), ecceTERA computes the score of a most parsimonious reconciliation (MPR).
::DEVELOPER
Computational Methods for Paleogenomics and Comparative Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26. PMID: 27153713.
:: DESCRIPTION
Burntrees is a script for manipulating tree (*.t, *.trprobs, *.con) and parameter (*.p) files from MrBayes (v.3). The script exctracts trees and (by default) the taxon translation table and the trailing “end;” from a MrBayes tree file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
iTree ,which is based on immunology knowledge, constructs whole-genome or whole-proteome based phylogenetic trees whithout sequences alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DensiTree is a program for qualitative analysis of sets of trees that make it possible to visually inspect the posterior distribution of an MCMC run over a tree. Many features of the posterior distribution are easily visible, such as agreement/disagreement of tree topologies, uncertainty in node heights and relative dominance of particular topologies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Remco R. Bouckaert.
DensiTree: Making Sense of Sets of Phylogenetic Trees.
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq110
:: DESCRIPTION
GIGA is an efficient tree building program that allows phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is used to generate trees in the PANTHER Classification System.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Jun 9;11:312.
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.
Thomas PD.
:: DESCRIPTION
The program RNAlocmin reads secondary structures to RNA sequence provided in file seq.txt (can be altered with “-s” option) and search for a local minima by performing a gradient walk.
::DEVELOPER
Theoretical Biochemistry Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HTTMM is a package designed for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1112-22. doi: 10.1109/TCBB.2015.2415814.
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.
Qiu YQ, Tian X, Zhang S.
:: DESCRIPTION
TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the version of TreeView available for the Mac Classic and Windows
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Page, R. D. M. 1996.
TREEVIEW: An application to display phylogenetic trees on personal computers.
Computer Applications in the Biosciences 12: 357-358.
:: DESCRIPTION
CNT-ILP implements a integer-linear program (ILP) for solving the Copy-Number Tree (CNT) problem. This problem aims to infer the copy-number tree of minimum cost from the copy-number profiles of distinct tumor clones.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R.
Complexity and algorithms for copy-number evolution problems.
Algorithms Mol Biol. 2017 May 16;12:13. doi: 10.1186/s13015-017-0103-2. PMID: 28515774; PMCID: PMC5433102.
