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Jevtrace2 (v3.12b)

The code has gone through a major overhaul enabling work with large datasets and streamlining functionality and usability. Jevtrace2 is distributed as a single executable JAR file with no installation required.

 

Introduction

Jevtrace is a implementation of the evolutionary trace method. The software expands on the evolutionary trace by allowing manipulation of the input data and parameters of analysis, and presents a number of novel tree inspired analysis of protein families. Jevtrace includes a multivalent graphical browser for multiple sequence alignment, phylogeny, and structure, as well as underlying object and algorithmic infrastructure.

Structure visualizaton is designated to WebMol , allowing live mapping of results onto protein structures. The combination of Jevtrace+WebMol can be used generically as a viewer for combinations of molecular phylogeny, sequence alignment, and structure data.

Jevtrace is platform independent and has been tested on

, , , .

Using a text-based sequence coloring format (SeqSel), Jevtrace graphical results can be saved and imported into other software:

- The UCSF Chimera Extensible Modeling System allows import of the SeqSel format through the MSF Viewer module module (explained here).

- Warren DeLano has kindly provided a script for applying SeqSel colorings to molecular structures viewed in his excellent program PyMol.

 

Licensing

Jevtrace is packaged and distributed with . The binary executables are free for academic use. Download here.

For commercial licenses please contact the UCSF Office of Technology Management (OTM).

 

Related links:

Groups

Computational Genomics Research Group, UC Berkeley

Evolutionary Trace Servers

Evolutionary Trace Report Maker @ Baylor College of Medicine

Multiple Alignment

ClustalX

Phylip

Databases

GPCRDB

 

Email bugs, comments, suggestions:


 Page last modified 03/08/13