SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool

SHOT 2.0

:: DESCRIPTION

SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.

HTTMM – Hierarchical Taxonomy Tree based Mixture Model

HTTMM

:: 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

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 HTTMM

:: 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.

TreeView 1.6.6 / TreeView X 0.5-1 – Tree Drawing Software

TreeView 1.6.6 / TreeView X 0.5-1

:: DESCRIPTION

TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from. The PHYLIP package contains tree drawing programs which offer a greater variety of trees than TreeView, but are somewhat clumsy to use. The forthcoming PAUP* for Windows does not have a graphical interface, hence TreeView allows you to create publication quality trees from PAUP files, either directly, or by generating graphics files for editing by other programs.

TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeView , TreeView X

:: 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.

RNAlocmin 2.0 – Finds local Minima of RNA + Constructs Barrier Tree

RNAlocmin 2.0

:: 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

Marcel Kucharík at Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • ViennaRNA

:: DOWNLOAD

 RNAlocmin

:: MORE INFORMATION

GIGA 1.4 – Gene Tree Inference in the Genomic Age

GIGA 1.4

:: 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

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Compiler

:: DOWNLOAD

 GIGA

:: 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.

DensiTree 2.2.1 – Qualitative Analysis of Sets of Trees

DensiTree 2.2.1

:: 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

Remco Bouckaert

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

DensiTree

:: MORE INFORMATION

Citation

Remco R. Bouckaert.
DensiTree: Making Sense of Sets of Phylogenetic Trees.
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq110

iTree – Immunopeptidome-based Tree of Life

iTree

:: DESCRIPTION

iTree ,which is based on immunology knowledge, constructs whole-genome or whole-proteome based phylogenetic trees whithout sequences alignment.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

 iTree

:: MORE INFORMATION

Splice 1.0.1 – Tree of Life

Splice 1.0.1

:: DESCRIPTION

Splice is an experimental and artistic puzzler. Immerse yourself in its microbial world and start splicing! Every level (“strand”) consists of a number of cells that you will need to rearrange into a target structure in several moves (“splices”). Exploration and experimentation are key in determining how the curious little cells react to each other.

::DEVELOPER

Cipherprime

:: SCREENSHOTS

Splice

:: REQUIREMENTS

  • iPhone / iPad / Android / PS3 / PS4 /Linux/ Windows/ MacOsX

:: DOWNLOAD

 Splice

:: MORE INFORMATION

branchCut 1.0 – Breaks long Branches in a Tree by adding Taxa

branchCut 1.0

:: DESCRIPTION

branchCut takes a phylogenetic tree and break longest branches until a certain number of taxa is reached.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 branchCut

:: MORE INFORMATION

Burntrees 0.2.2 – Perl script for manipulating MrBayes tree and Parameter files

Burntrees  0.2.2

:: 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

Johan Nylander 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 Burntrees

:: MORE INFORMATION