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.
Large Trees
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
| Sequence Data |
Trees can be built on either the nucleotide or amino acid sequences. |
| Distance Model |
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. |
| Marker |
A list of markers available in the chosen set of sequences. |
| Alignment Options |
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. |
| Photographs |
Option to include matching specimen photographs and spreadsheet of taxonomy for comparison. |
| Filters |
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. |
| Colour |
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. |
| Ambiguousߨ
ߨ Base/Gap Handling |
Complete or Pairwise Deletion options. |
| Result 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. |
| Page Orientation |
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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