BOLD includes core and extended tools to analyze specimen and sequence data.
All three of the core analysis tools have been improved with the new 3.6 version of BOLD. The Image Library now includes increased labelling and sorting options. The Distribution Map has been overhauled to allow to easier interactions with the data. The Taxon ID Tree also has new labelling options, and can perform larger builds.
Email Analysis results to allow for parallel workflows
Use the newly available option to run multiple analyses by having the results emailed when each analysis is finished.
Results can be stored for up to 4 weeks, saved for future comparison, and links to the results can be shared between collaborators.
This option is available on the parameters page for most of the BOLD analysis tools.
Illustration of the option to email results from analysis on the tool parameters page
Once images have been uploaded to a project, it is possible to view them in two ways. The first is by opening an individual record where any corresponding images will be displayed below the specimen data. The second is via the Image Library in order to view a group of specimens, as shown below.
The Image Library displays one image per specimen but allows users to choose a specimen orientation view in order to compare morphological differences between specimens. This tool is useful for diagnosing contamination or misidentification as taxonomy is displayed below each image. The specimens can be displayed sorted by identification or BIN. In the general options, users can also select how many images to display per row and per page.
Image Licensing is viewable upon mouse rollover. To view the attribution and further details on specific images, open the specimen data page from the record list.
Image Library (Lepidoptera)
(Displayed Specimen Images: Copyright 2010, Research Collection of Ulf Eitschberger)
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Distribution Map Analysis
The new Distribution Map plot the collection points for a selected set of specimens when geographic reference data is available. There are two versions available for use.
- GPS points are clustered on the map in coloured circles, and single records are signified by a blue marker. The circles indicate that there are multiple GPS points clustered there - hovering over these circles will display the bounds of the cluster. Green circles indicate that there is more than 1 point, yellow circles have more than 10 points, and orange circles have more than 100 points.
- The square symbol in the upper right corner of the map is a search tool that allows users to draw a rectangle on the map to select all the records that fall within that region. The records can then be searched on BOLD in order to allow users to download or run further analysis on that subset of records. It also allows users to edit records to quickly correct GPS points, if they are found to be incorrect.
- Users can zoom in out or on the map using their mouse scroll wheel, or with the plus/minus buttons provided in the upper left hand side. Clicking on one of the GPS cluster markers will zoom in to that cluster.
- The Interactive Map is built on the open-access platform OpenStreetMap and therefore can be published, re-used, and modified at the user’s discretion
- The Google Earth map is a display of the specimen collection points in the program Google Earth. This is free software that can be downloaded from the web. Google gives permission for use in publications as long as the Google logo remains on the image.
- The Google Earth map is a portable KML file download which can be shared among colleagues. It is available by clicking on the Open in Google Earth link at the top of the Interactive Map. This file has embedded specimen images, along with specimen identifiers, country, province/state, institution/collection information, and the Extra Info field.
Google Earth Map
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Taxon ID Tree
The Taxon ID Tree functionality allows for the generation of dendrograms from sequencing using the neighbor joining algorithm. Sequence alignment is automatically handled and multiple labeling options are available. This tool can be accessed by clicking on Taxon ID Tree under the sequence analysis panel on the Project Console and Record List pages.
Result of the analysis include a tree in PDF format for easy dissemination and publication, Newick format for rendering in other formats and layouts (i.e. circular), and a taxonomy report that provides a breakdown of the data used. When the option to include matching images and spreadsheet is selected, the system returns a spreadsheet with specimen identifiers and full taxonomy in the same order the records appear in the tree as well as the images of the specimens in the same order as the tree. Utilizing these options can help catch data entry and lab errors where samples may be swapped in plates. They are also useful for detecting misidentified specimens.
BOLD now provides the ability to built larger Taxon ID Trees , up to 12,000 COI sequences. For other markers and unaligned sequences, trees are limited to 3,000 sequences.
Taxon ID Tree parameter page
Parameters available for Taxon ID Tree
||Trees can be built on either the nucleotide or amino acid sequences.
||Kimura 2 Parameter is the default distance model. Other options are Jukes Cantor and Pairwise Distance.
|Tree Building Method
||Neighbour Joining is the only method at this time.
||A list of markers available in the chosen set of sequences.
||Alignment options include BOLD Alignment, MUSCLE, and Kalign.
|Terminal Branch Labels
||Selection of labels to add to the end of each branch including extra info, taxonomy, geography, identifiers, sequence details, and BIN identifiers.
||Option to include matching specimen photographs and spreadsheet of taxonomy for comparison.
||Can be applied to omit sequences below a given length (since very short sequences may skew the results), analyze only sequences with less than 1% ambiguous bases, or to exclude problematic sequences.
||The default is to colour problematic sequences in blue (stop codons present) and red (contaminations or are flagged by users). Other colourization options include: taxonomy, geography, extra info, Sequence age, or BINs.
ß¨ Base/Gap Handling
||Complete or Pairwise Deletion options.
||Option to view the results immediately or to have the results emailed when available. For larger trees, it is recommended that the email results option is used so the the users may continue to use BOLD while waiting on the tree to compile.
||Trees can now be displayed in landscape orientation
Standard Taxon ID tree (Lepidoptera) coloured by taxonomic family. The numbers following the species name map to the matching images and taxonomic spreadsheet for easy comparison.
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