Taxonomy & Phylogeny
Entrez Taxonomy (NCBI)
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
The taxonomy database contains the names of all organisms that have at least
one sequence (nucleotide or protein) in an NCBI database. The taxonomic tree
can be browsed to locate an organism. The taxonomy page for an organism contains
its lineage, links to available sequences, maps, and other available information
from NCBI resources. Links to external taxonomy resources are also included.
Also available on this site is an extensive list of taxonomy resources compiled
by the NCBI Taxonomy group: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=resources.
GRIN Taxonomy for Plants (USDA)
http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl
The
taxonomic data in GRIN provide the structure and nomenclature for the National
Plant Germplasm System (NPGS, ARS, USDA). All families and genera of vascular
plants and over 40,000 species from around the world, especially species that
are economically important, are included in GRIN. Database entries provide
information including scientific and common names, classification, distribution,
economic impacts, and references.
International Association for Plant Taxonomy/Smithsonian Institution-Index
Nominum Genericorum (ING)
http://ravenel.si.edu/botany/ing/ingForm.cfm
ING is a compilation of published generic names for all organisms covered
by the International Code of Botanical Nomenclature. ING includes bibliographic
citations and information about the typification and nomenclatural status of
generic names.
MEGA: Molecular Evolutionary Genetics Analysis
http://www.megasoftware.net/index.html
MEGA software can perform parsimony, distance matrix, and likelihood methods
for molecular data (nucleic acid sequences and protein sequences). It can do
bootstrapping, consensus trees, and other methods, as well as many types of
data editing tasks, tests of the molecular clock, and single-branch tests of
significance of groups.
NEWT (EBI)
http://www.ebi.ac.uk/newt/display?from=www&search=
NEWT,
a taxonomy database maintained by UniProt, integrates taxonomy data from NCBI
with data from the UniProt Knowledgebase. Each species record contains scientific
name, common name, synonym, lineage, and number of UniProt Knowledgebase entries.
Links to external resources are also provided.
The PHYLogeny Inference Package (PHYLIP)
http://evolution.gs.washington.edu/phylip.html
PHYLIP is a package of programs for inferring phylogenies (evolutionary trees).
The package includes several methods, such as parsimony, distance matrix, and
likelihood methods (bootstrapping, consensus trees, and others). The program
can handle molecular sequences, gene frequencies, restriction sites, and distance
matrices.
Phylogeny Programs
http://evolution.genetics.washington.edu/phylip/software.html
This site describes and provides links to almost 300 phylogeny packages. Program
lists can be browsed by methods used, computer systems, and many other variables.
Each entry includes a description and links. This list has been compiled by
the developer of the PHYLIP program.
TreeBASE: A Database of Phylogenetic Knowledge
http://www.treebase.org/treebase/
TreeBASE is designed to manage and explore information on phylogenetic relationships
It stores phylogenetic trees, data matrices, and bibliographic information
on phylogenetic studies. TreeBASE can be explored interactively using trees
included in the database.
The Tree of Life Web Project (ToL)
http://tolweb.org/tree/phylogeny.html
ToL is an international collaborative project. The project provides information
about the diversity of organisms on Earth, their characteristics, and their
evolutionary history (phylogeny). Each page contains information about a group
of organisms (e.g., echinoderms, tyrannosaurs, phlox flowers, club fungi).
The 4000 ToL pages are linked to each other in the form of the evolutionary
tree of life and illustrates the genetic connections between all living things.
The Universal Virus Database (ICTVdb, International Committee on Taxonomy
of Viruses)
http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm
ICTVdB is an Index of approved virus names linked to virus descriptions. It
also incorporates the plant virus database VIDEdB. The database is illustrated
with EM pictures, diagrams, and images of symptoms contributed by virologists
from around the world.
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