#Computer specifications. All programs were executed on:

Dell precision tower 7910
Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
Architecture x86_64
2 sockets, 10 cores per socket, 2 threads per core (40 CPUs), RAM: 128860

#Open source software developed by others

NAME  VERSION
bash	4.4.23
bwa   0.7.15-r1142-dirty
samtools	1.9 (using htslib 1.9-410-ge43b472)
picard-tools	2.7.1
SPAdes	3.10.1
eggNOG-mapper	1.0.3
FastQC		0.11.4
Trimmomatic	0.35
OrthoFinder	2.3.5
mafft		7.312
RAxML		8.1.24
BLAST+	2.2.31
fastANI	1.3
prodigal	2.6.3
Freebayes	1.0.2
GNU parallel	20180422
vcflib	41
CD-HIT	4.7
HMMER	3.1b2	

#Perl version and modules used (modules are also specified in the top lines of each perl-script)

perl v5.26.1
bioperl v.1.7.5
strict
GetOpt::Long
Pod::Usage
POSIX
List::Util
Bio::Seq
Bio::SeqIO
Bio::Align::AlignI;
Bio::AlignIO;
Bio::SimpleAlign;
Bio::Align::Utilities
Bio::SearchIO
Array::Utils


#R version and packages used within scripts (other packages are listed in "R.commands" files)

3.5.0
segmented
ggplot2
RColorBrewer
gplots
gridExtra
reshape
ape