Protocols

TAED specifications

Information


Unique identifier OMICS_03258
Name TAED
Alternative name The Adaptive Evolution Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline David Liberles

Publications for The Adaptive Evolution Database

TAED citations

 (2)
library_books

Extracting functional trends from whole genome duplication events using comparative genomics

2016
PMCID: 4862183
PMID: 27168732
DOI: 10.1186/s12575-016-0041-2

[…] mologous sequences are then placed within gene families based on a clustering algorithm such as single-linkage clustering. Pre-established gene families from gene family databases such as Ensembl [], TAED [, ], and Selectome [] may also be used, to which new sequences can be added using software like pplacer []. Multiple sequence alignments are generated using standard alignment algorithms which i […]

call_split

A systematic search for positive selection in higher plants (Embryophytes)

2006
BMC Plant Biol
PMCID: 1540423
PMID: 16784532
DOI: 10.1186/1471-2229-6-12
call_split See protocol

[…] ons occurred along the branch. This statistical assessment was refined through evaluation with a neutral null hypothesis, as described below. The procedure described above automatically generated the TAED database and hits were manually curated for this study. Manual evaluation of positively selected genes involved examination of the alignments, where in families with branches with Ka/Ks>1 and ali […]

TAED institution(s)
Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA; Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
TAED funding source(s)
Supported by National Science Foundation Grants DBI-0743374 and DBI-1355846 for support as well as the University of Wyoming INBRE Award P20RR016474.

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