This series of pages is a set of characterizations of all orders and families of extant angiosperms (flowering plants) and gymnosperms, i.e. all seed plants, as well as many clades grouping families and orders and some smaller clades, especially within larger families. They are designed to help in teaching seed plant phylogeny at a time when our knowledge of the major clades of seed plants and the relationships within and between them are still somewhat in a state of flux, even if much of the broad outline is becoming clear. Here I very largely follow the Angiosperm Phylogeny Group classification (APG 1999, 2003), although with one or two more orders and with a number of unplaced families in slightly more resolved positions in the tree - recent examples are Hydatellaceae, Perrottetia and Bhesa (Zhang & Simmons 2006). ... [Information of the supplier, modified]
This is a database of systematic literature on the Decapoda, compiled by the Assembling the Tree of Life: Decapoda project. You can search references online, or download the entire library as an Endnote-compatible reference library. In many cases, we are able to make the full text of the papers available as PDF files. The online references search will also give information on PDF availability. ... [Information of the supplier]
This database provides a snapshot of the current taxonomic distribution of nucleotide sequences in GenBank. Its purpose is to convey information about the potential phylogenetic data sets (clusters, or sets of homologous sequences) that can be constructed from the database for taxa of interest. It mirrors the NCBI taxonomy tree. The number of clusters is estimated by all-against-all BLAST searches and sequence clustering algorithms (for all nodes with < 35,000 sequences, and excluding sequences > 7500 nt in length). Model organisms are defined as any node (not subtree) having >100 clusters or more than 10,000 sequences. By default, sequence tallies for model organisms propogate upward in the tree along with nonmodel organisms, but this information can be excluded, so that users can get a sense of taxonomic breadth of the sequence diversity in the database. Note, however, that the bulk of "genomic" data for model organisms is not entered in the database at all (see below for types of sequences included). Cluster tallies are linked to a view of the data availability matrix for that node in the taxonomy tree, which can provide useful guidance for supermatrix and supertree construction. Sequences for each cluster can be downloaded as an unaligned FASTA file for further analysis. Provisional alignments and phylogenetic trees are also provided. ... [Information of the supplier]
Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v8.0, Phytozome provides access to thirty-one sequenced and annotated green plant genomes which have been clustered into gene families at eleven evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable. ... [Information of the supplier]
The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. On more than 3000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. Each page contains information about a particular group of organisms (e.g., echinoderms, tyrannosaurs, phlox flowers, cephalopods, club fungi, or the salamanderfish of Western Australia). ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things. ... [Information of the supplier]
TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships (Sanderson et al., 1993, 1994; Donoghue, 1994; Donoghue and Ackerly, 1996; Piel et al., 1996; Morel, 1996; Piel et al., 2000). Its main function is to store published phylogenetic trees and data matrices. It also includes bibliographic information on phylogenetic studies, and some details on taxa, characters, algorithms used, and analyses performed. The database is designed to allow retrieval and recombination of trees and data from different studies, and it can be explored interactively using trees included in the database. TreeBASE therefore provides a means of assessing and synthesizing phylogenetic knowledge. (...) The database currently includes 6106 authors, 2946 studies, 8462 trees, and 82043 taxa" (as of December 2011). ... [Information of the supplier]
