Frequently Asked Questions
1. How do I cite Explicet in my publications?
- Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, and Frank DN. Explicet: Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data. Bioinformatics (2013) 29 (23): 3100-3101.
2. How do I get the source for Explicet per the GPLv3 license?
The source of Explicet will be made available within the near future on SourceForge. A link will be posted here when this process is complete.
3. How do I know when new updates of Explicet are available?
Please register on the Explicet Forum (a Google Group): Explicet Forum. To receive an email notification when a new version of Explicet is released, make sure you are receiving "All email" in your Google Group settings. New releases will also be announced via the Welcome message at the Explicet Forum and at the top of the Explicet homepage. You can also visit our Coming Soon page to see our plans for new Explicet features.
4. How do I get help using Explicet?
Please register on the Explicet Forum (a Google Group): Explicet Forum. This is the most efficient way for us to interact with you and for you to see the issues and solutions found by other users of Explicet.
5. How do I install Explicet on Windows or Mac or Linux?.
6. What is the best way to learn to use Explicet?
Start by going through the Explicet tutorial which is automatically installed on your computer by the Windows, Mac, and Linux installation procedures. Explicet is available for installation via the Explicet Downloads page. The Explicet tutorial is placed in the Documents folder on Windows (My Documents on Windows XP). The tutorial is in Users/Shared/Explicet_Documents on the Mac. The tutorial is included in the Linux installation tar ball. The Explicet tutorial (and the two data files it references) are also available for download separately here: Tutorial Files.
7. How much does Explicet cost?
Explicet is a free to use, open source software package licensed under the terms of GPLv3. See: Copyright and GPL License.
8. Who do I contact to ask about paying for customized features in Explicet?
Contact Chuck Robertson via the email address on the Copyright and GPL License page to get the process started.
9. I think I found a bug in Explicet. What do I do?
Please report any issues you think might be related to bugs in Explicet via the Explicet Forum: Explicet Forum. We will make best efforts to help you through the problems. However, note well the standard terms for all software licensed under GPLv3: "This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE".
10. When I double click on a ".otu" file on a Mac, an older version of Explicet starts up. How do I fix this?
- This is a "feature" of MacOS which automatically keeps track of which applications go with which extensions. To solve this, you may need to completely remove all older versions of Explicet.
11. Are previous versions of Explicet available?
Previous releases of Explicet (starting with version 2.8) are available here: Explicet Previous Releases.
12. When I import a Qiime OTU Table, the hierarchy pane in Explicet lists each different OTU Name as a separate line... No hierarchy is shown. Why?
This occurs because Explicet assumes that a "/" character exists between each of the taxonomic categories in the OTU Names in an OTU table. However, Qiime uses the ";" character. To fix this, in the Import OTU Table Counts dialog, just change the character in the box labeled Use this character as the OTU Name delimiter: from a "/" to a ";".
13. How do I extend Qiime taxonomy results to include the Qiime OTU IDs?
The Qiime OTU ID is the name returned after sequence clustering per the usual Qiime sequence-handling process. In some cases, the cluster ID may provide precision beyond that obtained via the default taxonomic identification by RDP Classifier. Often > 30% of the cluster representatives will have "Unassigned" taxonomies. Appending the Qiime OTU ID to the Qiime taxonomy is one way to preserve the clustering information. This is done as follows:
- Open your Qiime OTU Table (.txt file) in a spreadsheet program (ex. Microsoft Excel)
- Create a new column at the very end with a column heading such as "taxonomy with OTU ID"
- In the second cell (row 2) of the "taxonomy with OTU ID" column, enter:
- where L2 = the cell in row 2 that contains the Qiime "taxonomy"
- and A2 = the cell in row 2 that contains the Qiime "OTU ID"
- Drag the corner of the cell down (or use the fill down command) to copy the formula to each row of your data in the OTU table
- Export the spreadsheet as a tab separated value file: File → Save As → File Name, Save as type: Text (Tab delimited) (*.txt)
Open Explicet and import this .txt file: File → Import → OTU Table Counts → select the .txt file you just created
- On the OTU Table Counts dialog that appears, you need to make a couple of changes:
Change Use this character as the OTU Name delimiter: from a forward slash to a semicolon (from "/" to ";")
Edit this dialog so only one Column Type is labeled as OTU Name (double click on the item to be changed - it will turn into a drop down list - click on the drop down and select do not import this column)
When you are done, only the column that you created in Excel, labeled "taxonomy with OTU ID", should be assigned to OTU Name
- The Qiime OTU table with the OTU IDs appended to the taxonomy lines should now appear in Explicet
14. Why are some metadata items missing from samples after import?
- If you find that your metadata did not import as expected, open your metadata .txt file in a text editor. Check the file for delimiting characters such as commas. If your file contains any of these characters, remove them, then save the file and retry the import into Explicet.
15. When I toggle between Show Libraries and Show Sorted Libraries in alpha diversity, nothing happens.
The library order will not update in the plot setup window of alpha diversity until Bootstrap is clicked again; for changes to take effect, rerun Bootstrap.