TreeFam (Tree families database) is a database of
phylogenetic trees of animal
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s. It aims at developing a curated resource that gives reliable information about
ortholog and
paralog
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...
assignments, and
evolutionary
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation t ...
history of various
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
families.
TreeFam defines a
gene family as a group of genes that evolved after the speciation of single-
metazoan
Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in ...
animals. It also tries to include outgroup genes like
yeast
Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to consti ...
(''S.cerevisiae'' and ''S. pombe'') and
plant
Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
(''A. thaliana'') to reveal these distant members.
TreeFam is also an
ortholog database. Unlike other pairwise alignment based ones, TreeFam infers
orthologs
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spe ...
by means of gene trees. It fits a gene tree into the universal
species
In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual
curation
Curation may refer to: Activities
* Content curation, the collection and sorting of information
* Data curation, management activities required to maintain research data
* Digital curation, the preservation and maintenance of digital assets
* Evi ...
, and infer complex
ortholog and
paralog
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...
relations.
The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex
phylogenies
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
. TreeFam-A families are manually
curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families.
TreeFam is being run as a project at the
Wellcome Trust Sanger Institute
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
It is located on the Wellcome Ge ...
, and its software is housed on
SourceForge
SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirrori ...
as "TreeSoft".
See also
*
Homology (biology)
In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of p ...
*
HomoloGene
*
Phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
*
OrthoDB
OrthoDB presents a catalog of orthologous protein-coding genes across vertebrates, arthropods, fungi, plants, and bacteria. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates or ...
*
Orthologous MAtrix (OMA)
*
Inparanoid
References
{{reflist, 1
External links
TreeFam websiteTreeSoft
Computational phylogenetics
Genetics databases
Genetics in the United Kingdom
Phylogenetics
Science and technology in Cambridgeshire
South Cambridgeshire District