Table 6.

Databases and software used in this study.

Name	URL	Version or accession date
Bowtie2	https://www.github.com/BenLangmead/bowtie2	2.3.3
BLAST	ftp.ncbi.nlm.nih.gov/blast/executables/blast+/	2.2.28
Cytological bands	ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/	2015-11-20
FASTQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/	0.11.5
Figtree	http://tree.bio.ed.ac.uk/software/figtree/	1.4.1
Geneious	https://www.geneious.com/
GenomeTools	http://genometools.org/pub/	1.5.1
GIMP	http://www.gimp.org/downloads	2
GRCh38	ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/	2014-08-27
HMMER	http://hmmer.janelia.org	3.1b1
Htslib	https://github.com/samtools	1.5-22-g7a6854b
JAVA		1.8.0-144
jModelTest	(D Darriba) https://github.com/ddarriba/jmodeltest2	2
MACSE	(V Ranwez) http://www.mybiosoftware.com/macse-1-01b-multiple-alignment-of-coding-sequences.html	1.01b
Pfam-A	ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz	2014-09-05
ProtTest	(D Darriba) https://www.github.com/ddarriba/prottest3	3
RAxML	https://github.com/stamatak/standard-RAxML	7.2.8
Repbase	(J Jurka) http://www.girinst.org/repbase/	19.07
RSYNC	https://rsync.samba.org/	v3.0.6 protocal v30
Samtools	https://github.com/samtools	1.5-9-g473d6a4
Sratoolkit	https://github.com/ncbi/sra-tools	2.8.2-1
Trimmomatic	https://github.com/timflutre/trimmomatic	0.36