Difference between revisions of "ETE3"

Revision as of 20:33, 30 January 2017

Description

ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It provides a wide range of tree handling options, node annotation features, programmatic access to the phylomeDB database (containing thousands of pre-calculated phylogenetic trees), and automatic orthology and paralogy detection. In addition, ETE implements an interactive tree visualization system as well as a highly customizable tree drawing engine to create PDF and SVG tree images. Note that, although ETE is mainly developed as a tool for phylogenetic analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree.

Required Modules

System Variables

HPC_{{#uppercase:ete3}}_DIR - installation directory

Additional Information

This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs

Basic usage:

module load gui
launch_gui_session --module ete3 -e launch_ete3

Connect with xpra locally using the xpra command

xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713

Citation

If you publish research that uses ete3 you have to cite it as follows:

ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046

Revision as of 20:25, 30 January 2017 (view source) Maxprok (talk \| contribs) (Created page with "Category:Software Category:Biology Category:Phylogenetics {\|<!--CONFIGURATION: REQUIRED--> \|{{#vardefine:app\|ete3}} \|{{#vardefine:url\|http://etetoolkit.org/}} <!--CO...")		Revision as of 20:33, 30 January 2017 (view source) Maxprok (talk \| contribs) Newer edit →
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−	ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It provides a wide range of tree handling options, node annotation features, programmatic access to the phylomeDB database (containing thousands of pre-calculated phylogenetic trees), and automatic orthology and paralogy detection. In addition, ETE implements an interactive tree visualization system as well as a highly customizable tree drawing engine to create PDF and SVG tree images. Note that, although ETE is mainly developed as a tool for phylogenetic analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree.	+	ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It provides a wide range of tree handling options, node annotation features, programmatic access to the phylomeDB database (containing thousands of pre-calculated phylogenetic trees), and automatic orthology and paralogy detection. In addition, ETE implements an interactive tree visualization system as well as a highly customizable tree drawing engine to create PDF and SVG tree images. Note that, although ETE is mainly developed as a tool for phylogenetic analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree.