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Protocols

TreeFam specifications

Information


Unique identifier OMICS_05340
Name TreeFam
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 9
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/TreeFam

Maintainer


  • person_outline Fabian Schreiber

Additional information


http://www.treefam.org/help

Publication for TreeFam

TreeFam citations

 (101)
library_books

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

2018
BMC Genomics
PMCID: 5896114
PMID: 29642853
DOI: 10.1186/s12864-018-4647-4

[…] ariance among different organisms and to further scrutinize the five species genome-specific genes identified by Ensembl Compara, we also used HomoloGene (https://www.ncbi.nlm.nih.gov/homologene) [], TreeFam (Release 9, March 2013, 109 species, 15,736 families) (http://www.treefam.org/) and OrthoDB v9 (http://www.orthodb.org/) and assessed orthology based on RBH (reciprocally best hit, performing […]

library_books

Draft genome of the Peruvian scallop Argopecten purpuratus

2018
GigaScience
PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] s initially implemented by the alignment of an “all against all” BLASTP (with a cutoff of 1e-7) and subsequently followed by alignments with high-scoring segment pairs conjoined for each gene pair by TreeFam_3.0 []. To identify homologous gene pairs, we required more than 30% coverage of the aligned regions in both homologous genes. Finally, homologous genes were clustered into gene families by Or […]

library_books

Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus

2018
GigaScience
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] The gene families were identified using TreeFam software (Tree families database, RRID:SCR_013401) [] as follows: BlastP was used to compare all the protein sequences from 8 species: A. planipennis, A. glabripennis, O. taurus, D. ponderosae […]

library_books

The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain

2018
BMC Genomics
PMCID: 5778671
PMID: 29357812
DOI: 10.1186/s12864-018-4448-9

[…] rformed using LastZ []. To compare the level of coding sequence divergence between these two species, we analyzed the gene coding sequence variance between possible orthologous genes identified using TreeFam []. This involved as following steps, which has been widely used to identify orthologous genes: Firstly, protein sequences of these two species were compared by blast with the E-value threshol […]

call_split

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca

2018
Sci Rep
PMCID: 5772498
PMID: 29343788
DOI: 10.1038/s41598-017-18378-8
call_split See protocol

[…] Annotated nuclear genes of C. variabilis, A. protothecoides, Helicosporidium sp., P. cutis, and P. stagnora were classified into known gene families using TreeFam 9 with an E-value cut-off of 1E-5. Plastid-related proteins were identified using PRIAM (March 2015) with an E-value cut-off of 1E-10. […]

library_books

Genome wide protein phylogenies for four African cichlid species

2018
BMC Evol Biol
PMCID: 5784529
PMID: 29368592
DOI: 10.1186/s12862-017-1072-2

[…] e longest protein isoform and amino acid sequence for each gene. This was done to limit the phylogeny to one representative protein isoform for each gene. To assign each of these proteins to a single TreeFam family, we utilized the treefamscan.pl script provided as part of the TreeFam API []. This script uses the program HMMER to identify matches using hidden Markov model profiles generated for ea […]

Citations

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TreeFam institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
TreeFam funding source(s)
Supported by Wellcome Trust [WT077044/Z/05/Z], The Wellcome Trust [WT098051]; BBSRC [BB/I025506/1], European Molecular Biology Laboratory, European Community’s Seventh Framework Programme (FP7/2007-2013) [222664]. (‘Quantomics’).

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