ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.
NUCPLOT is a program that automatically generates schematic 2D representations of protein-nucleic acid interactions. The input is a standard PDB file and the output is a colour or black-and-white PostScript file which gives a simple, at-a-glance representation of the hydrogen bonds and hydrophobic contacts between proteins and nucleic acids.
NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:
1. primary sequence
2. known or predicted secondary structure
3. known or predicted tertiary contacts (optional)
Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.