Software
DSBplot
DSBplot is a Python 3 program for processing and visualizing high-throughput amplicon sequencing data obtained to study double-strand break (DSB) repair due to the nonhomologous end-joining (NHEJ) repair mechanism.
For the latest version, please see GitHub or PyPi.
DNA Tensegrity Triangle
Listed below are programs used in "Engineering Tertiary Chirality in Helical Biopolymers".
SDRAP
SDRAP is a web application which annotates DNA segments in DNA rearrangement precursor and product genomes which describe the rearrangement, and computes properties of the rearrangements reflecting their complexity. The annotated segments sought by the software are analogous to MDSs, IESs, and pointers in ciliate DNA rearrangements.
Assembly Words
This application draws the assembly graph, chord diagram, and circle graph defined by the word.
dnagrep
dnagrep is grep-like tool to visualize
genome searches and output to various media formats (printable, interactive, and audio).
dnagrep acts as a digital highlighter to aid in visualization of patterns within DNA sequences.
News: August 2014 -- Security enhancements
STAGR
Software To Annotate Genome Rearrangements
genus.py
Tool to compute genus range and spectrum of double occurrence words.
Chord Diagram Genus Spectrum
Calculates the chord diagram genus spectrum using javascript.
Draw Legal Strings
Draws the arrangement of segments of two genes corresponding to a two-gene legal string.
