This repo should be considered pre-alpha. It may or may not be updated.
This project aims to provide some tools to aid in genetic archeology and understanding. Given a 5-to-3 FASTA DNA sequence, a codon translation table in NCBI format, and a mutation profile in the custom .mprof mutation file format, it will attempt to aid in determining whether the sequence has been mutating around a similar configuration or a different one. It will do this by using a 'robustness' number from 0-1, indicating the probability that a given codon frame will express the amino acid (or start/stop codon) in question after mutation, approximated by considering all mutations down to a given relative probability, and assuming the potential for infinite mutation. Example mutation spectrum is a slightly edited version of the data presented in Lee et al.'s "Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing", doi:10.1073/pnas.1210309109
Anyone may use this tool for non-commercial use. This tool is provided without any warranty or guarantee.
For any inquiries and feedback; Contact e-mail: [email protected]