List of all programs utilised and their version:

Prodigal - version 2.6.3
HMMER - version 3.1b2
MMSeqs2 - version 5fcc48fbf4f6697e73e1e2a4b3f53c6cdf87e8f1
Parasail - version 2.1.5
Famsa - version 1.1
LEON-BIS - version 1.0
OD-SEQ - version 1.0
HH-suite - version 3
hhblits - version 3.0.3
MMSeqs2 taxonomy program - version b43de8b7559a3b45c8e5e9e02cb3023dd339231a
CD-HIT - version 4.6
RaxML - version 8.2.12
Papara - version 2.5
pplacer - version v1.1.alpha19-0-g807f6f3
SEQKIT - version 0.10.1
EPA-NG modeltest-ng - version 0.3.5
Taxtastic - version 0.8.9
BWA mapper - version 0.7.12
BEDTOOLS - version 2.23.0
MCL - version 12.068
seqkit - version 0.7.2
seqtk - version 1.2-r102-dirty
bbmap - version 35.14
openmpi - version 1.8.1
datamash - version 1.3
ripgrep - version 0.10.0
parallel - version 20200122
igraph - version 0.7.1