PlantAligDB: A database of curated nucleotide sequence alignments for plants

The PlantAligDB is a comprehensive on-line resource of curated nucleotide sequence alignments for plant research. The website provides a complete, quality checked and regularly updated collection of alignments that can be used in taxonomic, molecular genetics, phylogenetic and evolutionary studies.

Asteraceae CC-BY-SA-3.0 > Explore different genomic regions.
> Search for a plant family.
> BLAST search against all nucleotide sequences.
> Download curated alignments.
> Upload your datasets.
> Retrieve genetic diversity indices.
> Visualize and edit phylogenetic trees.

 By Crusier (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

Database content

Nº of different families: 223
Nº of sequences: 66052
Nº of alignments: 514
 Families with more alignments:
Asteraceae
Orchidaceae
Poaceae
 Largest sequence alignment:
Fabaceae (2599 trnL GH sequences)

Our nucleotide sequence alignments were carefully selected to represent different genomic regions and plant families with at least 10 species.

PlantAligDB current statistics (updated March, 2017):
Genomic region Genome Type Nº of sequences Nº of alignments/families
atpF-atpH cpDNA Inter-genic spacer 1025 31
psbA-trnH cpDNA Inter-genic spacer 4852 79
trnL CD cpDNA Intron 2527 44
trnL GH cpDNA Intron 34674 173
rbcL cpDNA Protein-coding gene 1748 39
matK cpDNA Protein-coding gene 11341 113
ITS nuDNA Transcribed spacers and 5.8S gene 9885 35


Taxonomic groups
Family atpF-atpH psbA-trnH trnL CD trnL GH rbcL matK ITS Number of Regions
Asteraceae 62 275 283 1955 126 603 1155 7
Brassicaceae 14 16 176 1236 98 58 6
Cupressaceae 17 17 133 17 23 118 6
Iridaceae 22 61 15 518 210 350 6
Orchidaceae 21 68 40 1538 16 1038 51 7
Orobanchaceae 24 57 320 12 102 10 6
Poaceae 181 425 397 2078 107 476 830 7
Polygonaceae 49 12 215 19 58 39 6
Rosaceae 22 228 21 766 273 581 6
Rubiaceae 11 115 335 1427 42 49 6


Genetic diversity

Recent news

-Last update:09-07-2018.
-Wasabi PAGAN merge alignments tool example added.
-Wasabi PAGAN and PRANK phylogenetic tree calculation example added.
-ITS alignments added to PlantAligDB.
-The PlantAligDB project is launched (09-03-2017).

How to cite

"A web-based platform of nucleotide sequence alignments of plants"
Chiara Santos, João Carneiro, and Filipe Pereira
Submitted to Molecular Ecology Resources