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BLAST-EXPLORER helps you building datasets for phylogenetic analysis

Alexis Dereeper12, Stephane Audic1, Jean-Michel Claverie1 and Guillaume Blanc1*

Author Affiliations

1 Information Génomique & Structurale - CNRS-UPR2589, Institut de Microbiologie de la Méditerranée - IFR 88, 163 Avenue de Luminy, 13009 Marseille, France

2 Current Address: INRA - UMR 1097, DIA-PC "Diversité et adaptation des Plantes Cultivées", 2 Place P. Viala, 34060 Montpelllier - France

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BMC Evolutionary Biology 2010, 10:8  doi:10.1186/1471-2148-10-8

Published: 12 January 2010



The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task.


To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the platform.


BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at webcite