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
Databases
Email bugs, comments, suggestions:
Page last modified 03/08/13