Treefam
Encyclopedia
TreeFam is a database of phylogenetic tree
s of animal gene
s. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene
families.
TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast
(S.cerevisiae and S. pombe) and plant
(A. thaliana) to reveal these distant members.
TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species
tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation
, and infer complex ortholog and paralog 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. 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 Sanger Institute
, and its software is housed on Sourceforge
as "TreeSoft".
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
s of animal gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
families.
TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
(S.cerevisiae and S. pombe) and plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
(A. thaliana) to reveal these distant members.
TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation
Collection catalog
In museums and archives, the collection of objects or material is normally catalogued in a collection catalog . Traditionally this was done using a card index, but nowadays it is normally implemented using a computerized database and may even be made available online.- External links :* from the...
, and infer complex ortholog and paralog 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. TreeFam-A families are manually curated
Collection catalog
In museums and archives, the collection of objects or material is normally catalogued in a collection catalog . Traditionally this was done using a card index, but nowadays it is normally implemented using a computerized database and may even be made available online.- External links :* from the...
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 Sanger Institute
Sanger Institute
The Wellcome Trust Sanger Institute is a non-profit, British genomics and genetics research institute, primarily funded by the Wellcome Trust....
, and its software is housed on Sourceforge
SourceForge
SourceForge Enterprise Edition is a collaborative revision control and software development management system. It provides a front-end to a range of software development lifecycle services and integrates with a number of free software / open source software applications .While originally itself...
as "TreeSoft".
See also
- Homology (biology)Homology (biology)Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
- PhylogeneticsPhylogeneticsIn biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
- OrthoDBOrthoDBOrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny...
- Orthologous MAtrix (OMA)Orthologous MAtrixOMA is a database of orthologs extracted from available complete genomes.The orthology predictions of OMA are available in several forms:* OMA Pairs: for a given gene, a list of predicted orthologs in other species is provided....