GramAlign is a time-efficient progressive Multiple Sequence Alignment (MSA) algorithm. The novelty of GramAlign comes from the sequence distance estimation step, whereby distances are determined by the natural grammar present in nucleotide and amino acid sequences.
GramCluster is a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
GramDist is a utility for generating dissimilarity matrices using the relative complexity measure, a computationally efficient and alignment free evolutionary distance metric.
RAIphy is a semi-supervised metagenomic fragment classification program. It utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI).
Mimosa is a time-efficient phylotyping method using metagenome reads for the estimation of the microbial diversity and the abundance profile associated with an environmental sample.
nSpect is an exploratory visualization tool for inspecting high-dimensional proximity data.
ICYK is a grammar inference algorithm inspired by the classic CYK sequence classification algorithm. It is currently intended for use in analyzing DNA/RNA sequences in order to identify possible secondary structures.