EMBL European Bioinformatics Institute

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(Release 9, March 2013, 109 species, 15,736 families)

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
(see the BRCA2 gene family page as an example).

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(HMM-based protein sequence search vs. TreeFam & Pfam HMMs)
Insert into tree
Insert into TreeFam gene tree using

Parsimony (蚂蚁海外加速器永久免费版super-fast, citing_treefammight insert into several branches)
Maximum Likelihood (citing_treefammore accurate, 雷霆加速器ios永久免费might take a bit longer)

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Species Tree used in TreeFam 9. See full tree here.

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  • citing_treefam Feature: TreeFam family visualisation available: [...]
    (posted 19 Feb 2014)
  • citing_treefam Feature: Tree Insertion available: [...]
    (posted 9 Sept 2013)
  • citing_treefam Suggestion: Downloading the full gene tree view: [...]
    (posted 3 May 2013)
  • citing_treefam Suggestion: Domain diagrams as hyperlinks to Pfam: [...]
    (posted 3 May 2013)
  • citing_treefam旋风加速器ios [...]
    (posted 3 May 2013)
  • citing_treefam TreeFam: What is in the next release: [...]
    (posted 10 December 2012)
  • citing_treefam We are on the move: [...]
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  • citing_treefam游戏加速器教程_手游加速器免费下载_biubiu加速器:2021-6-15 · biubiu加速器教程频道为各位玩家提供最新的游戏加速器免费版下载，热门手游免费加速教程，手机游戏加速器操作技巧等信息，找更多加速器内容就来biubiu加速器官网。旋风加速器ios永久免费
    (posted 27 March 2012)

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Learn about how TreeFam builds families, alignments, and trees and how families defined in TreeFam.


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TreeFam families
There are many ways you can link to TreeFam data. Learn how you can link to e.g. our gene families.

Gene tree widget
You can add our gene tree widget to your website: e.g. simply point an iframe to our trees using a TreeFam family ID or a sequence identifier.


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Protein domains:
RNA families:
Repetitive DNA: 永久免费加速
Peptidases:
Spurious ORFs: 海外加速器永久免费ios

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Data download
Download all our data: e.g. alignments, hmms, trees, pairwise orthologs, external references and more.

API
Programmatically fetch data through our API and see a list of example scripts in our 永久免费加速. Use treefamscan to score your sequences against TreeFam hmms.

Citing
If you find TreeFam useful, please consider citing the references that describe this work:
TreeFam: 2008 Update Jue Ruan, Heng Li, et al. Nucleic Acids Research (2008)
doi: 10.1093/nar/gkm1005