Here are some of my favourite tools, and scripts/programs that I have written or helped to develop.
I helped to develop the tool “OLGenie” for detection of purifying selection in overlapping genes, published in MBE in 2020. We have applied this program in various virus genomes, and are increasingly applying it to prokaryotic genomes. We also have some ideas for developing this and other OLG detection methods further.
I do most of my work with bash or python scripts incorporating these key programs:
Bowtie2 – for mapping NGS data to genomes
Samtools – for manipulating mapped NGS data
BEDTools – for matching sets of genome features to each other.
Evolutionary sequence analyses:
ETE3 – for phylogenetic tree visualisation and manipulation on the command line
Newick Utilities – for easy command-line manipulation of phylogenetic trees
IQTREE – for fast tree building
Most minor text file manipulations can quickly be conducted on the command line with the under-rated standard GNU/bash tools such as awk.