MoSeC (Model to Sequence Converter) is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence.
The XXmotif web server can discover motifs that are enriched in sets of nucleotide sequences provided by the user. XXmotif uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.
LDDist is a Perl module implemente in C++ that enables the user to calculate LogDet pair-wise genetic distances based on amino acid as well as DNA/RNA sequences