Table of Contents. DiversiTree Tutorial! 1 of 29

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1 DiversiTree Tutorial! 1 of 29 Table of Contents Part 1: The DiversiTree Application Overview... 2 Search Pane & Search Categories... 3 Result & Data Windows... 4 Trace Archives... 5 User Created Lists... 6 Saving/Loading Data... 7 Part 2: From Sample to SNP From Sample to SNP... 8 Tree Sample Search Category... 9 Tree Sample Results Window Tree Sample Detail Window DNA Extraction Detail Window Sequencing Plate Detail Window Sequence Chromat Detail Window Sequence Assembly Detail Window SNP Data Part 3: Bulk Data Retrieval Bulk data Retrieval Data Retrieval Process... 21

2 DiversiTree Tutorial! 2 of 29 Overview DiversiTree is a web-based application designed to provide intuitive search-based access to Pine Genome data generated through the ADEPT2 and CRSP resequencing projects. The primary focus of DiversiTree is to provide easy intuitive access to every level of resequencing information, from Tree Sample to SNP. DiversiTree is comprised of four major parts: the Search Pane, the Results Window, the Detail Window, and the Data. In all cases, users begin with by selecting a Search Category for the Search Pane, fill in the search fields, and search. From there, DiversiTree generates a Results Window. The items listed in the Results Window may be clicked in order to display a Detail Window, which then leads the user to a variety of data. Currently, DiversiTree allows users to search based on the following Categories: EST (GenBank) Contigs Primers Sequencing Reactions Tree Samples DNA Extractions Sequencing Chromats SNP

3 DiversiTree Tutorial! 3 of 29 Search Pane & Search Categories The Search Pane on the left side of the DiversiTree window contains a list of Search Categories, one for each type of information previously listed. Clicking on a Search Category causes that category to expand. Upon expanding, the user is presented with various input fields that they may use retrieve a listing of results. Typing information into a text box and selecting or deselecting individual species allows the user to filter out data that does not match their search criteria. While the search is running, a spinning progress wheel will appear next to the listing of results. For best results, do not perform other searches while there is a progress wheel anywhere on the screen. a completed search Once the search is complete, the progress wheel will disappear and be replaced with the total number of results that match your search criteria. If there are fewer than 1000 results, a button labeled Display will appear, which can be clicked to view search results in a results window.

4 DiversiTree Tutorial! 4 of 29 Result and Data Windows Both results and data windows function like windows on most standard computers. By clicking and dragging the bar on the window, a user can reposition the window. Similarly, by clicking and dragging the bottom right corner of the window it can be resized. Windows will automatically be provided with a scroll-bar on the right hand side if one is required to view all contained information. Results Window When a user brings up a results window, all of the data in our database matching the associated search criteria will be displayed in the window in a tabular format. The headings of the table can be clicked on to re-order the results. Double clicking on a particular row will bring up a data window. Multiple data windows can be brought up at the same time by clicking on a row and shift + clicking on another row to select a many consecutive rows or by ctr + clicking on another row to pick and choose specific rows. Once all desired rows are selected, clicking on the View Selected button will bring up data windows for all selected rows. Data Window A data window provides the Database Interface s most detailed view of the data. Each type of data will have different attributes associated with it and thus will have different rows displayed. Some of our data is linked to other data. Links are denoted by green boxes around text and can be clicked on to bring up a data window for the associated information.

5 DiversiTree Tutorial! 5 of 29 Trace Archives Raw DNA Trace data is available for viewing and download through the DB Interface. DNA Trace Files The DNA Trace files may be downloaded from a Sequence Assembly detail window, or from a Sequencing Chromat detail window. The DNA Trace data files are all grouped into compressed TAR/GZ archives. The uncompressed DNA Trace files themselves are provided in both AB1 and SCF formats. Chromatogram Viewer The Chromatogram Viewer allows users to view trace archive data without needing to download files or install files. Users who have trace file software may choose to download the data and view it from their own machine.

6 DiversiTree Tutorial! 6 of 29 User Created Lists User Created Lists are windows that allow users to store a collection of results or data windows in a list. This is useful for users who want to save some data to look at later or create their own groupings of data in easily accessible lists. To create your own list, simply click on the black button at the bottom left corner of the screen and select Create Window. A text box will appear in the middle of the screen prompting for a name. Once a name has been provided and accepted, a new contentless window will appear. To fill the list, simply drag other windows and drop them onto the list. In addition to dragging windows onto the list, selecting multiple rows from a results window and then dragging those rows onto the list will also populate the list. To expand items that are in a list simply click on the name of the item and a window will be brought up. a list with 4 primers dragging multiple rows into a list

7 DiversiTree Tutorial! 7 of 29 Saving/Loading Data Saving your progress with the interface is a simple but somewhat involved process. The first step is to click on the black plus button in the bottom-left corner of the screen and select Save Workspace. Once this is done, a text box will show up containing all of the data required to recreate all windows as they currently appear. Select all of this text and copy it. Open up your favorite text editor (Notepad or TextEdit work best) and paste into a new document. Save the document somewhere and your session is saved. In order to load your data again, simply open up the document that you saved and copy the information contained therein. Then go into the DB Interface and click on the black plus button and select Load Workspace. A similar text box to the Save Workspace option will appear. paste the text into this text box and click ok. Your saved windows and their locations will be returned.

8 DiversiTree Tutorial! 8 of 29 From Sample to SNP DiversiTree can be used to retrieve a wide variety genetic information. However, at its core it is an organizational system that allows users to traverse the resequencing process from Tree Sample to SNP. The image below depicts one such example of a search that flows from Sample to SNP., and in the pages that follow, we will traverse this arbitrary path, from window to window, through the resequencing process until we have reached a SNP.

9 DiversiTree Tutorial! 9 of 29 Tree Samples Search Category We begin by expanding the Tree Samples search category, which is embedded in the Search Pane.

10 DiversiTree Tutorial! 10 of 29 Tree Sample Results Window After clicking the Display button, DiversiTree displays a Results Window listing each Tree Sample associated with Pinus Syvestris.

11 DiversiTree Tutorial! 11 of 29 Tree Sample Detail Window Double Clicking on a Tree Sample prompts a Tree Sample Detail Window to appear. This window lists specific information about the tree itself, and displays a listing of all DNA Extractions performed on this sample. Notice the Sent for Sequencing: Yes/No message embedded in each DNA Extraction line. This message indicates whether or not the specific DNA Extraction has been sent for resequencing, and eliminates the need for you to click-and-check each one of them.

12 DiversiTree Tutorial! 12 of 29 DNA Extraction Detail Window Clicking on a DNA Extraction record prompts the DNA Extractions Detail Window to appear. This window displays detailed information about the particular extraction. It also displays information detailing how the sample was plated before being sent for resequencing.

13 DiversiTree Tutorial! 13 of 29 Sequencing Plate Detail Window Clicking on a Sequence Plate link brings you to a Sequence Plate Detail Window. This window provides a list of Chromats that were sequenced from this specific sequence plate well.

14 DiversiTree Tutorial! 14 of 29 Sequence Chromat Detail Window Clicking on a Chromat link leads to the Sequencing Chromat Detail Window, which displays information about this specific chromat. Clicking the Chromatogram: View link loads the chromatogram sequence into a web-based chromatogram viewer for easy inspection. You may also download the chromatogram archive associated with this Sequencing Chromat.

15 DiversiTree Tutorial! 15 of 29 Sequence Assembly Detail Window Clicking on the Sequence Assembly link leads you to the Sequence Assembly Detail Window. This window provides a listing of Sequencing Chromats used to construct this assembly, and a listing of discovered SNPs.

16 DiversiTree Tutorial! 16 of 29 SNP Data Finally, clicking on the SNP link brings you to the SNP Data Window, which displays information about the particular SNP.

17 DiversiTree Tutorial! 17 of 29 Bulk Data Retrieval Various search fields have a List Upload icon placed next to them. A typical example looks like this: When this button is pressed, a Bulk Uploader window appears:

18 DiversiTree Tutorial! 18 of 29 Each individual Bulk Retrieval Window performs a unique data retrieval function, but they all share the same common structure and components. They all require the user to provide a list of IDs (such as GenBank Accessions, Contig IDs, SNP IDs, etc) in the form of an Excel CSV file. They each provide a set of output options for the user to choose from, and they all produce Excel CSV files for the user to download. The first component shared by every Bulk Retrieval Window is the File Selector component shown in the figure below: This section allows the user to select an input file that contains the list of IDs that the user has chosen to retrieve data for.

19 DiversiTree Tutorial! 19 of 29 The second set of common components that appear in each Bulk Retrieval Window are the Output Selection Fields. These fields are comprised of checkboxes that allow the user to select which data they would like to appear in their final output file.

20 DiversiTree Tutorial! 20 of 29 The third common component found in every Bulk Retrieval Window is the Species Filter. This dropdown menu allows users to select their species of interest and retrieve data that pertains only to that specific species. If the user chooses the All option, then data pertaining to all species will be added to the final output file.

21 DiversiTree Tutorial! 21 of 29 Data Retrieval Process The first step involved in using Bulk Data Retrieval system is to create an Excel CSV file containing a list of target IDs. The following example spreadsheet contains a list of Contig IDs.

22 DiversiTree Tutorial! 22 of 29 The next step in the process is to save the file in CSV format by choosing File > Save As, and selecting the CSV format option.

23 DiversiTree Tutorial! 23 of 29 Next, open the desired Bulk Data Retrieval window and upload your list of IDs.

24 DiversiTree Tutorial! 24 of 29 Next, checkmark each of the desired Data Output fields.

25 DiversiTree Tutorial! 25 of 29 Next, click the Submit button and leave the window open while it processes your request.

26 DiversiTree Tutorial! 26 of 29 After the Bulk Data Retrieval window completes its processing, a results page will be displayed. Results may be downloaded from this page.

27 DiversiTree Tutorial! 27 of 29 A typical Annotations Results file contains one column of data for each Data Output field marked by the user. The original list is also IDs is displayed in the first column.

28 DiversiTree Tutorial! 28 of 29 If the user requests sequence data, then a FASTA formatted sequence file will be provided for download on the results page.

29 DiversiTree Tutorial! 29 of 29 If the user requests Trace File data, then a compressed arechive of Trace Data will be provided for download from the results page. Please note that these files need to be decompressed before they can be used.