RED-T: an application utilizing the Ratio of Evolutionary Distances for determination of alternative phylogenetic events
Welcome to my project web page! We have developed a method, termed RED, to analyze the evolutionary history of individual genes and the potential of lateral gene transfer (LGT). A preliminary description of this method was presented briefly at our poster (ASM 2001).
A c c e s s t h e R E D - T H E L P d o c u m e n t a t i o n
RED-T is a Java application for phylogenetic analysis that is based on a unique method, RED, that utilizes the ratios of evolutionary distances to distinguish between alternative evolutionary histories (Farahi et al. 2003). RED-T, Ratio of Evolutionary Distances for determination of alternative phylogenetic events, allows the user to examine if any given experimental gene shares the same evolutionary history as the designated control gene(s). Moreover, the tool detects any differences in evolutionary history, and allows the user to examine comparisons of Ed for a likely explanation. Lateral gene transfer (LGT), which may have a significant influence in organismal evolution especially in prokaryotes evolution, is one mechanism that could explain the findings of these RED-T analyses. RED-T can be downloaded below. In addition to the application, complete interactive access to 60 genes is provided. These genes include many aminoacyl t-RNA synthetases and ribosomal proteins.
Three Java tools are available below. These tools are:
RED-T application package - RED-T application package includes the most recent software and should be sufficient for most investigators. Supplemental ANALYSES package, which contains the 60 gene samples analyzed during our investigation, is also available.
RED-T web-based applet - original version and processor of the tool available for long-term users
The Matrix Integrator - This applet converts matrix formatted data into the columnar format recognized by RED-T (organism1,organism2 tab value). This feature is also implemented in the RED-T application.
If you are a first time user, we would appreciate it if you would register before downloading/using any of these tools. This registration is largely for record keeping and notification of any updates, but we also welcome your comments and suggestions.
| Contents of the files |
Downloadable files |
Approximate size of file |
| RED-T application only * | RED-Tv2.1.18.exe | ~ 627 KB |
| ANALYSES folder only | RED-T_Analyses.exe | ~ 1.461 MB |
| RED-T application bundle including the ANALYSES folder * | RED-Tv2.1.18_full.exe | ~ 2.041 MB |
| RED-T source codes (class files) | RED-Tv2.1.18_source_code.exe | ~ 200 KB |
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* Help file (help.htm) is included in these downloads, which also can be accessed online. |
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This application can be accessed in two different ways. First, the application can be downloaded to your machine. Second, the application can be launched from this web site. If you use this method, only the analyses and not the tool will be saved to your machine. Lastly, the source code is also available for downloading.
This application is created and distributed as a JAR file. It requires JRE 1.4 or later. Visit java.sun.com to obtain the latest JRE.
The complete RED-T application package requires downloading both the RED-T tool and the optional Analyses folder.
HELP documentation which includes FAQ, feature descriptions, and more... is available as part of the application. Also, it can be accessed from this web site: click here.
Download RED-T application package
If prompted to 'OPEN' or 'SAVE' the file, choose to 'SAVE'.
This is distributed as an
self-extracting file (RED-T_2.1.x.exe).after downloading the latest RED-T package, you must extract it.
run the *.exe file (Windows: double click on it),
choose a folder on your computer to extract the contents of the package.
this operation maintains the file structure that is essential for operation of the application, as seen in the example folder content below:
To launch RED-T, double click on the RED.jar file within the folder.
...this package includes the current help files, but not the "ANALYSES" folder which contains the 60 genes analyzed during our investigation (in "Samples" folder).
To download ANALYSES folder, link here and save the "Analyses.exe" file.
To extract the ANALYSES folder, run the *.exe file and choose the folder where the RED.jar is for extracting. in the same location as the RED.jar file and next to the VisualNumerics folder.
Below is the content and file structure of the ANALYSES folder:
Remember that all other files and folders, except the "ANALYSES" folder, which is not essential for the operation of the application, are required in the same directory as the RED.jar for the application to launch.
Also, a larger file, which contains the ANALYSES folder and the RED-T application can be downloaded here. Extract the contents to a folder on your machine and you are ready to run RED-T.
Launch it from here! (to be implemented)
If prompted to 'OPEN' or 'SAVE' the JAR file, choose to 'OPEN'.
Remember if you use this method, only the analyses and not the tool will be saved to your machine.
Download the source code for the latest RED-T version
this includes all *.class files.
extract by running the *.exe file and choose a location on your computer to extract it to.
RED-T applet (web-based form predecessor of the RED-T application)
launch the applet from this link only if the location (path) of the data file is known. Otherwise, to use the applet with our data files select one of the links below.
Data files available for use with the applet includes these 69 genes:
The same ribosomal protein and aminoacyl tRNA synthetase genes are also available within the ANALYSES folder of the latest version of the RED-T application, which can be accessed above.
RED's Matrix Integrator applet
This applet converts matrix formatted data into the columnar format recognized by RED-T (organism1,organism2 tab value). This feature is also implemented in the RED-T application.
CONTACT INFORMATION: [ back to top ]
Department of Microbiology, University of Georgia
Department of Microbiology, University of Georgia
mailing address: Department of Microbiology, University of Georgia, Athens, GA 30602-2605 (USA)
telephone: 706.542.4692
e-mail: kfarahi@uga.edu
/ or use our feedback form /
Unpublished work ©2002 The University of Georgia Research Foundation, Inc.
