v1.3

2 changes:

• fixed multi-threading for all steps (tested with Python 3.10.9)
• new output file 'unclassified_proteins.txt' generated at step3 and containing the names of all unclassified proteins (only tested with example_dataset)

v1.2

major update:
_ new parameter to select the phylogenetic method (nj, me or ml)
_ new parameter to optimise the species overlap approach (i.e. how orthologous groups are delineated in phylogenetic trees)
_ better memory management at step3
_ tables output at step3

v1.1

alignements are built from DIAMOND CIGAR strings (the version requires Diamond v0.9.30+)

v1.0

initial release