TreeFam (Tree families database) is a database of

phylogenetic tree 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 ...

s 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 ba ...

s. It aims at developing a curated resource that gives reliable information about

ortholog 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 spec ...

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 heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...

history of various

families. TreeFam defines a

gene family A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on ...

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 constitut ...

(''S.cerevisiae'' and ''S. pombe'') and

plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclud ...

(''A. thaliana'') to reveal these distant members. TreeFam is also an

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 spec ...

by means of gene trees. It fits a gene tree into the universal

species In biology, a species is the basic unit of 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 the appropriate s ...

tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex

and

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 G ...

, 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, mirrorin ...

as "TreeSoft".

References

{{reflist, 1

External links

TreeFam website

TreeSoft
Computational phylogenetics Genetics databases Genetics in the United Kingdom Phylogenetics Science and technology in Cambridgeshire South Cambridgeshire District

See also

References

External links