jMOTU

jMOTU is a handy, easy to use package specially designed to help you cluster barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website.
jMOTU does the following:
· reads input sequences in FASTA or NEXUS format
· calculates distances between pairs of sequences using a combination of BLAST and the Needleman-Wunch exact global alignment algorithm
· clusters input sequences into MOTU using various cutoff measures
jMOTU can process large datasets and uses a series of filtering steps to minimise the number of exact global alignments that must be performed. When calculating pairwise distances, jMOTU ignores gaps and counts only nucleotide mis-matches, making it relatively robust to sequencing errors caused by homopolymer runs. Clustering is carried out using a greedy algorithm that is not dependent on input sequence order. JMOTU has been tested on raw datasets of around 50,000 input sequences, and can cluster larger datasets by preforming preclustering of subsets of data before combining them for a global analysis.System requirementsJava