Features

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See also a list of Screen shots.

Content management

OTU pages
Create OTU pages (e.g. species pages) by creating content types (or using built in types) and including them in templates. Mix and use content in any number of templates. Create formalized taxon pages or use internally for lab notes.

Choosing the categories to include in a content template.


Content can be created and cloned or moved to other OTUs. For example a draft created then cloned to and refined for each OTU.

An OTU page with content for a given template.


Pages can be managed internally then published to publicly accessible sites.

An OTU page (species page) as seen publicly.

Matrices

Characters
Characters can be annotated with tags, figures and other linkages.

Showing a character.

Otus
Matrices can be populated with OTUs via a number of different ways allowing for easy reformulation and testing.

Managing the OTUs in a matrix

Coding
Matrices can be coded with a one-click method allowing for rapidly transitioning across rows or columns. Notes and figures document the finer details of the character in question.

Coding a matrix.


Specimen management

Specimens
Individual specimens can be identified by any number of identifiers (e.g. barcodes), and determinations.

Showing a specimen record.

Lots
Specimens can also be managed as lots. Individual specimen records can be extracted from lots as need be.

Showing a lot record.

Taxonomic hierarchies

Taxonomic names
Create taxonomic catalogs. The taxonomic hierarchy is shared across projects. Permissions to add or edit names are set by node in the taxonomic tree.

Showing the taxonomic history for a species name.


Sequence handling

Sequences
Manage sequence data. Export to Nexus, fasta and other formats.

Annotating a list of sequences.

References management

References
Manage references including associated pdfs. References can be shared across projects.

Editing the entry for a reference.

Associations

Associations
Create associations among OTUs chaining any number of them linearly, give them confidence levels and associate supporting data.

Showing an individual association.

Images

Images
Load and store images locally.

A page of images.

Morphbank images
Images stored on Morphbank can be easily linked to and used as if they were local.

Searching and associating Morphbank images with OTUs in mx.


Keys

Bifurcating keys
Create and illustrate bifurcating keys. Text can be automatically linked to a glossary/ontology.

Editing a key couplet.


Multiple entry keys
Matrices can be used as multi-entry keys.

Using a multi-entry key.


Phylogenetics

Trees
Phylogenetic trees in Newick format can be stored and tied to datafiles and matrices. They can be viewed with Phylowidget.

Using Phylowidget to view a tree.

Trees are parsed to a relational format in addition to a Newick string. This functionality provides a foundation for experimental visualization and querying of phylogenetic relationships.

A tree as a nested set.


Ontology

Ontology
Simple ontologies can be created and illustrated. Functionality for exporting to OBO format and import from OBO are variously developed. See here for more.

Showing a term and its relationships.


And more...

There are also some older screen shots available, though the layout has evolved.

Personal tools