Welcome to RED-T (version 2.1.x) Help Page
This help page is to provide information for general use and explanation of various features of the RED-T application.
software requirements
installation instructions
Features
Taxonomic selection partition
RED Wizard
Frequently Asked Questions
How can I find out which version of this application I am using?
I can download the archive files (*.exe), but cannot extract (unpack) or open the archive files.
How can I find out what operating system or type and version of browser I am using?
After downloading, when I launch (start) RED.jar, the splash screen comes up only.
The box-selection (neon-green square) does not select plots I want.
I cannot import an image of a tree using the import feature.
I get an error every time I am importing a columnar formatted data.
What are some features planned for implementation in future versions?
How do I suggest a feature to be implemented in the future versions?
WHAT IS RED, AND HOW IS IT DIFFERENT FROM RED-T?
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.
The figure below is a screen shot of the RED-T application. The main window is separated into three resizable partitions: The main partition contains the plot generator as illustrated here in highlight mode and a bar displaying quantitative variables that reflect values for the selected portion of the plot. The second partition contains a text box for taking notes of analysis. The last partition contains five tabbed windows to provide different levels of taxonomic selection. In addition, the floating window displays an imported phylogenetic tree. Illustrated here is the analysis of the isoleucyl-tRNA synthetase gene, in highlight mode. High K values resulted from comparisons between bacterial clades B1 and B2 (outlined box), suggesting that one of these clades obtained its gene from another domain. It is clear that the eukaryote and bacterial clade B2 (arrows in plot and tree window) comparisons had much lower K values than the eukaryote and bacterial clade B1 comparisons, thus bacterial clade B2 was the likely recipient of the eukaryotic isoleucyl-tRNA synthetase (IleRS) gene.
RED-T is not distributed as an executable (*.exe), but as a JAR file (RED.jar). Since JAR is operating system independent (can be used with Windows, Apple, Linux), all that is need to run this application is JAVA Runtime Environment (JRE) 1.4 or above. If your machine does not have this version of JRE, it will attempt to retrieve and install the latest JRE. If you would like to download and install it yourself, find the latest JRE along with installation instructions at the Sun Microsystems web site, java.sun.com.
If you don't know which operating system or platform is running on your machine, you can click the below buttons to retrieve this information, along with information about your browser type/version and monitor.
Since the tool is currently distributed as a zip file, a software to decompress this file, such as WinZip is necessary. For more information go to the following link (Winodows XP has this uncompression tool built in)
There is no installation required.
If you are downloading the tool (packaged as an archive file), then follow these easy steps:
- If prompted to 'OPEN' or 'SAVE' the file, choose to 'SAVE'.
- After downloading the latest RED-T package, unpack it. To unpack it, double click on the *.exe file and choose a directory, and/or a folder such as "RED" to download into. This maintains the file structure that is essential for operation of the application.
- To launch (start) RED-T, double click on the RED.jar file...
- Choose from different packages, with one including the "ANALYSES" folder which contains the 60 gene samples analyzed during our investigation (in "Samples" sub-folder).
- To download ANALYSES folder, link here and save the "...Analyses.exe" file.
- Then unpack like above insructions.
- Then place (save) the ANALYSES folder in the same location as the RED.jar file (next to the VisualNumerics folder).
Remember that all files and folders are required to be in the same directory as the RED.jar for the application to launch.
If you are launching the tool from your browser, then don't worry about a thing. Your browser will do everything for you. Just click on the active link for the application, and it will launch if your browser has JRE 1.4 or above.
File Menu items:
New - this item starts the RED-T wizard that provides the user with three options: import new data to compare with the default control, import new data with the current control, or generate a new control.
Open - this item allows the user to open a previous plot saved under the 'Analyses' folder. In order to open a analysis saved by a previous version of RED-T (i.e. applet), use the 'New' menu item to import using the wizard.
Save and Save As... - these items allow the user to save the current analysis in a project folder under the 'Analyses' folder. The control used, the imported experimental data, the merged comparisons (Raw data), taxonomical mapping information identified during control/experimental development, and the notes taken are saved under this folder. 'Save as...' allows the user to specify a name for this project folder. 'Save' item automatically saves the project as the previous name, or uses the name specified under wizard protocol.
Import tree - this feature allows the user to import a graphic of a tree (or any other graphic such as a table, screenshot, plots, or pathways) to assist in the phylogenetic analyses. The images are imported into the floating Tree Image window. This window is turned on by the View menu item. Note that all graphics have to be in GIF or JPEG (JPG) formats.
Print - This item allows the user print different parts of the analyses. The user is given a list of items that can be printed - Plot & Calculations (checked as default), Notes, Organisms (content of the Organisms tab), and Raw data.
View Menu items: (these items can be turned on/off during analysis)
Tree Image - this item displays the imported tree image, which is either imported by the File Menu's Import Tree option, or an image already stored in the project folder. Remember that this image can be a table, plot, or any other image that the investigator would like to have during analysis.
m-line - allows for further interpretation of the mean of K values. Two lines are drawn through the origin with the slope equal to the mean of K (m). One (red colored) is immobile and reflects the m value of the displayed plots, which equals the quantitative variable displayed. The other line (gray colored) is able to pivot about the origin to make comparisons to the immobile line (red colored). This allows the investor to visually see the differences between various data (other clusters or individual plots).
Refresh/Select All/Clear All buttons - These button are found in the top left corner above the main partition. The 'Refresh' button allows the user to update the plot with any changes, such as selecting a new set of data or clearing the previous view. 'Select All' button allows the user to select all possible comparisons, and 'Clear All' button clears the plot completely.
Plot Zoom - this feature allows the user to zoom in and out of the plot by setting the range of the x and y-axes in evolutionary distance (Ed) units.
Boxed-selection feature - this feature allows a user to obtain the identification of all data points within a boxed area. This feature does not need to be turned. To use it, select the part of the plot for identification by holding the (left) mouse button and dragging the mouse from left to right.
Main partition - this window displays the current plot, including the labeled axes and data selected.
Quantitative variables bar: this bar is found immediately below the main partition and includes the sample size or number of values (n), mean of K (m), standard deviation of K (SD), and relative standard deviation (rSD), which is the SD of K divided by the m of K. K is the ratio of Ed of the experimental gene (y-axis) divided by the mean Ed of the control genes (x-axis) for each pair of organisms. The values for the selected data are shown in red font, while the values for all of the data are in parentheses.
- Intra-group and Inter-group tabs: in order to evaluate evolutionary relationships between taxonomic groups, the intra-group and inter-group tabs are available. For instance using these tabs, it is possible to compare genes from the archaeal domain to genes from the proteobacteria.
The intra-group comparisons tab, allows the user to compare within a group or taxonomic level. For example, if you would like to see all comparisons within Crenarchaeota, then expand the Archaea domain label by one level (click on the "+" next to Archaea) and click or highlight the sub-domain Crenarchaeota.
Similarly the inter-group comparisons tab contains two panels which allows the user to compare between groups. For example, if you would like to see all comparisons between Crenarchaeota and Bacteria, then click or highlight the Crenarchaeota in one of the panel and click or highlight the Bacteria in the second panel.
The levels of taxonomy is modeled after EMBL and ERGO databases. The tree-file structure can by expanded by clicking on the "+", and collapsed by clicking on the "-" next to each label.
Organisms tab - this window identifies the data currently being displayed or analyzed. Every organism for which data is available is listed. When the data is selected, the box in the first column is checked. The second column contains the abbreviation (RED-id's) for each organism used during importing of data. When the data is selected, the RED-id turns into a bold red font. The third column contains the genus and species identification for each organism. The fourth column contains the taxonomic hierarchy for each organism. The last column is the original identification code or accession number every sequence from the original imported data. The third, fourth and fifth column is color coded for each of the three organismal domains - green for Archaea, blue for Bacteria, and purple for Eukarya.
- n-Comparisons tab - this window allows the user to select specific data points for analysis. Each row includes a box for selection of the data point, the RED-id's of the two organisms being compared, the x and y coordinates of the data point, and the y/x ratio.
- Raw data tab - is just that, raw data! This is the data as read by RED-T as it loads a plot. So if you like to cut and paste from this window and save it for your reports, this is the place to do it. This is also a good place to see the list of selected data because only the selected data is displayed. Each row contains the RED-id's of the two organisms being compared, the x and y coordinates of the data point, and the y/x ratio.
Wizard for importing your own experimental gene:
TUTORIAL (coming soon!)
Opening an existing Analyses
Importing new experimental data to compare with RED-T' default control
Importing new experimental data to be compared with a developed control
Developing a new control
FREQUENTLY ASKED QUESTIONS (FAQ)
Why do I need to register before I use these tools?
If you are a first time user of RED-T and plan to download any of the RED-T tools, we encourage you to register by completing the feedback form. This is not mandatory! This is only for record keeping and notification of any updates. We also welcome your comments and suggestions via this form. Tell us what you think about the RED-T tools, Help files, our web sites, etc.
Where can I get more information on this application?
For more information on RED-T, see Bioinformatics publication, Farahi et al. 2003. The RED method manuscript is submitted and await press annoucement, meanwhile please contact us for a copy of the manuscript.
The box-selection (neon-green square) does not select plots I want.
Make sure the highlight mode is not on while choosing the area to select. Since the highlight mode displays all data, including the data not currently being analyzed, it does not see the data that is not active (black in highlight mode). Basically you are selecting empty space. Turn off the highlight mode by un-checking the box below the menu bar.
Why are the plot axes different for different plots?
The plot adjusts to the range of the data provided. It will add one Ed unit to the max value of every axis. To change these initial settings, adjust the axis ranges by using the Zoom feature below the Menu bar.
How can I find out what version of this application I am using?
From the main menu, choose About... from the Help Menu item. The application's splash screen will have the version assignment in the bottom left, under "RED-T".
How can I obtain RED source code?
All of the *.class files can be downloaded sepratly from the RED-T package downloads. In the same download menu, click on the link for RED-T_2.1.x_source_code.exe and download this archive file to your machine. Please read the licensing rights before making any changes to the code.
I can download the archive (*.exe) file, but cannot extract (unpack) or open the archive file.
You probably do not have an extracting software, like WinZip or WinRAR, installed on your machine. Go to download.com and download WinZip, WinRAR or another software that can unpack archive files.
If this is not the problem, then you might have downloaded a corrupt RED-T file. Please attempt another download before contacting us via email or the feedback form.
How can I find out what operating system or type and version of browser I am using?
Use the below diagnostic buttons to retrieve information on your browser type/version, operating system or platform, and resolution information of your monitor.
After downloading, when I launch RED.jar, the splash screen comes up only.
First, make sure that the file structure is as instructed by this page. If the same thing happens, this indicates that you do not have JRE version 1.4 or above installed on your machine. Please follow the instructions in software requirements to install the latest JRE on your machine.
I cannot import an image of a tree using the import feature.
If the image is not in GIF or JPEG (JPG) format you will not be able to import the file. In order to transform your image into one of these acceptable formats, use a graphic editor to save as either of these formats.
I get an error every time I am importing a columnar formatted data.
This is a formatting error that you will encounter if the file you are importing is not recognized by the wizard. There are two common errors:
- Make sure that the first line of the columnar format file begins with "....RED". If importing data from older versions, such as the applet, you must add this manually. The "....RED" is followed by the x and y axis labels in this format:
....RED(x-axis label,y-axis label)
....RED(control_default,Pro-tRNA synthetase)
- The columnar data must be in correct format. Each line should contain information exactly like this:
organism1,organism2 tab x-axis coordinate tab y-axis coordinate tab ratio return-carriage
RAA00970,RAB00502 0.906 0.99 1.092
How do I add a new organisms to RED-T' organisms list?
Hopefully you would not have to since we will update the list to reflect publicly available genomes. The only way to do this is to update the org_list.txt file. This will be in the same location as the RED.jar file. Follow the delimited format of this text file, beginning with an capitalized abbreviation, genus and species name, and so on.
What are the licensing rights for RED?
RED-T was developed during research at The University of Georgia, Department of Microbiology. All rights reserved. Currently, RED-T is
Unpublished work ©2002 The University of Georgia Research Foundation, Inc.
For more details or updates on the licensing of RED-T, please contact us.
Citing RED-T in literature or other works:
Farahi K, Whitman WB, and Kraemer ET. RED-T: application for utilizing the Ratio of Evolutionary Distances for determination of alternative phylogenetic events. Bioinformatics. 2003. 19:2152-4.
What are some features planned for implementation in future versions?Any feedback would be appreciated. Please describe the problem you have experienced in as much detail as possible. Provide as many operational steps as possible that led to the error. Fill out the feedback form, or if you are more comfortable, just email us. In your email, please include the application version. Please enter "Bug report" in the subject field of this email. We will update you with the fix as soon as possible.
Future versions will include more features to improve the phylogenetic data analysis. These include:
Tree generator: allows the user to generate phylogenetic trees and interactively compare them with the RED plots. This feature allows a user to import a Newick-standard formatted data and generate a tree. This tree will be interactive with the plot. The user can use this feature to compare a phylogenetic history of a gene with the RED plot.
Symbolizer: organismal shape designation for clear identification of displayed data.
Mouse over identification mode: allows individual plot identification to improve identification of the organismal distribution.
How do I suggest a feature for implementation in the future versions?
Any feedback would be appreciated. Please describe the feature you are suggesting and its range of application. Fill out the feedback form, or if you are more comfortable, just email us. In your email, please include the application version you are using. Please enter "Feature suggestion" in the subject field of this email. We will follow up with you as we attempt to implement your idea.
What features are planned for the next RED-T release, v.2.2?
One feature that will be implemented in the next version (v2.2) is to have a choice of symbols for every organism in the plot. This feature will be added to the Organisms List window, next to each RED-id. The user will have a variety symbols to choose, such as open and closed circles, squares and other geometric shapes. This will assist in the analyses of the plot by visually distinguishing the clades or clusters.
Kamyar Farahi - Department of Microbiology, University of Georgia
email: kfarahi@uga.edu
Eileen T. Kraemer - Department of Computer Science, University of Georgia
email: eileen@cs.uga.edu
telephone: 706.542.5799
William B. Whitman - Department of Microbiology, University of Georgia
email: whitman@arches.uga.edu
telephone: 706.542.4219
Unpublished work ©2002 The University of Georgia Research Foundation, Inc.