Archive for the ‘Phylogenetic Trees’ Category

taxize: Taxonomic search and phylogeny retrieval [R]

Monday, December 17th, 2012

taxize: Taxonomic search and phylogeny retrieval by Scott Chamberlain, Eduard Szoecs and Carl Boettiger.

From the documentation:

We are developing taxize as a package to allow users to search over many websites for species names (scientific and common) and download up- and downstream taxonomic hierarchical information – and many other things. The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names. General functions in the package that don’t hit a specific API don’t have two words separated by an underscore, e.g., classification. You need API keys for Encyclopedia of Life (EOL), the Universal Biological Indexer and Organizer (uBio), Tropicos, and Plantminer.

Just in case you need species names and/or taxonomic hierarchy information for your topic map.

Working with Trees in the Phyloinformatic Age

Monday, February 28th, 2011

Working with Trees in the Phyloinformatic Age by William H. Piel discusses the processing and display of phylogenetic trees.

The PhyloWidget that is mentioned in the slides can be found at: Phylowidget

If you are working on topic maps in bioinformatics, this should be on your list of works to review.

I was particularly amused by the advice given at the Phylowidget site in its step-by-step instructions:

* If you are a biologist: we recommend starting with the First Step and moving forwards.
* If you are a developer: we recommend starting with the Last Step and moving backwards.