Browse MOLE-BLAST documentation.

Getting started

A guide to MOLE-BLAST


MOLE-BLAST is a new tool to classify multiple query sequences and discover their relationship to each other. This tool provides a taxonomic context for the queries. It is intended to work with a specific locus from a set of organisms rather than sequences like the entire genome of an organism or unannotated contigs. Example input would be 16S sequences from different bacteria or ITS sequences from fungi. Currently, MOLE-BLAST only accepts nucleotide queries.

MOLE-BLAST has a multistep pipeline:

  • First, MOLE-BLAST groups the query sequences by locus using BLAST[1].
  • Second, it performs a BLAST database search to identify each query's nearest neighbors.
  • Third, it computes a multiple alignment (using MUSCLE [2]) for each locus, including query sequences and their nearest neighbors.
  • Finally, MOLE-BLAST presents the results of its analysis as a phylogenetic tree for each locus.

Further details about MOLE-BLAST are available at


[1] Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. PubMed

[2] Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time andspace complexity. BMC Bioinformatics. 2004 Aug 19;5:113. PubMed