How to Use the Database

• See the list of taxa
• Search the taxa by:
  
  • genus and/or species
  • taxonomic level
  • character state(s)
• Get NEXUS files
• Add or edit taxa (for contributors)
• Data organization (septum/septal pore)
• Character and character state descriptions
• Frequently asked questions

Home Page

See the list of taxa

Users may view an alphabetical list of the species in the database. Note that some entries whose taxonomic placement is uncertain are lacking one or more classification levels. Genera and species enclosed in parentheses (e.g. "(Ampelomyces) (quisqualis)) denote the anamorphic name when the teleomorphic name is unknown or uncertain.



Clicking on any of the taxon links from Phylum to Genus will list all the taxa below that classification level. Clicking on a species will call up that organism's page.

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Search the taxa

To start a search, a data set must be chosen. The user decides what structure's data to search, and in some cases, which coding method (multistate or binary).

Once the data set is selected, the organisms in the database can be searched using up to three criteria:

• genus and/or species - Partial or complete genus and species names can be entered into the text field.
• taxonomic level - A search can be limited to a particular classification level using selections from pull-down menus.
  
  
  
• character states - A search can be limited to species with one or more specific character states. For the Septum Database, a subgroup must be chosen first, e.g. Ascogenous hyphae/ascus, immature.
  
  
  Once a subgroup is chosen, two additional menus will appear. The first contains the characters applicable to the selected subgroup. When a character is chosen, the possible character states appear in the second menu.
  
  
  When the desired subgroup, character, and character state have been selected, click the "Add" button and that character state is added as a search criterion under the "Currently selected states" heading.
  
  
  More character states can be added to a search, or they can be deleted by clicking the corresponding "Remove" button.
  
  
  

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Get NEXUS files

Character state data of one or more species can be displayed as a functional NEXUS file from the Search Results page.

Data for each species listed in the search results are associated with one or more character locations or cell types. Clicking on the location code/cel type will open a window containing a NEXUS file with the character state data for that character location only. Non-applicable characters are indicated as missing data.

The NEXUS files generated from a search can be merged together by the web site into a single NEXUS file. When the search results first appear, every resulting NEXUS file has a check in the box next to its location/cell type code link, indicating that it has been selected for merging. Files are selected and unselected manually by clicking on the small boxes. Clicking the "None" button removes checks from all boxes. The button then changes to read "All", and clicking it will put checks in all the boxes.

Once the desired NEXUS files have been chosen, click on the "Download NEXUS file of Selected" button.

A window opens with the NEXUS file text of the merged data, which may be copied and pasted as needed. Here is an example of a merged NEXUS file.

Note that NEXUS entries of the same organism with different location codes are NOT MERGED into a single entry, but have separate entries, as seen in file excerpt image below. It is up to the user to create a single entry for analysis.

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Home Page

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Questions and/or Comments can be directed to

davem@umn.edu