github

INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) is a versatile software tool that extracts data values from sequencing reads and translates them into sequencing reads of another structure according to a user-defined process configuration file.

github

QUEEN is a framework to generate quinable and efficiently editable nucleotide sequence resources to resolve many current issues in building DNA. QUEEN enables to design a new DNA by using existing DNA resource files and records the construction process in an output file (GenBank file format). The GenBank files generated by QUEEN are able to regenerate the process codes that perfectly clone themselves and bequeath the design history to successive DNA constructs that recycle their partial resources. QUEEN-generated GenBank files are compatible with the existing DNA repository services and software.

github

FRACTAL (framework for distributed computing to trace huge accurate lineage) is a new distributed computing framework that is designated to reconstruct a large lineage of DNA sequences that have evolved or diversified from an ancestral DNA sequence through the accumulation of mutations.

github

PRESUME is a software tool that simulates cell division or speciation and diversification of DNA sequences in the growing population.

github

A Python script used for the base editing prediction in the following paper.

github

SPADE is a software tool to explore various periodic repeat regions from large genomic and protein data resources in a high-throughput and unsupervised manner.