Tag: Phylogenetic Analysis

TreeDyn 198.3 – Dynamic Graphics & Annotations for Phylogenetic Analyses

TreeDyn 198.3

:: DESCRIPTION

TreeDyn is a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.

::DEVELOPER

GEMI Bioinformatics F. Chevenet

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

TreeDyn

:: MORE INFORMATION

Citation:

Chevenet F., Brun C., Banuls A.L., Jacq B. and R. Christen
TreeDyn: towards dynamic graphics and annotations for analyses of trees
BMC Bioinformatics 2006, 7:439

Filo 1.1 – Simulate Sequence Data used in Phylogenetic Analyses

Filo 1.1

:: DESCRIPTION

Filo is designed to be used to simulate (molecular) sequence data used in phylogenetic analyses under very general conditions, including:

  • insertions and deletions; Insertions and deletions are propagated through the tree so the output file can be made to be the “true” alignment. This is very handy for checking out alignment methods, and is one of the main motivations for writing this program.
  • different phylogenetic histories (trees) along a sequence;
  • arbitrary rate matrices for each tree;
  • definition and re-use of node, branch, tree and global parameters;
  • output in various formats for subsequent analysis, e.g. in phylogenetic inference programs;
  • generation of trees under standard models such as Yule and All Trees Equally Likely.

::DEVELOPER

Dr. Michael Charleston

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

Filo

:: MORE INFORMATION

This software is intended for use in generating simulated sequence data for phylogenetic analysis. It is released as is, and with no warranty of any kind. Use it at your own risk!