Table 6. Analysis software versions and parameter settings.
| Software tool | Reference | Version | Parameters used* | Comments |
| FASTQC | [60] | v0.10.1 | ||
| fastq-mcf | [61] | ea-utils.1.1.2–537 | −l 51 -q 20 –qual-mean 20 -R | |
| Blobology | [37] | 2013-10-21 | default | |
| Khmer | [62] | khmer-17-05-2013 | -k 20 -C 20 -p | |
| Velvet | [63] | 1.2.08 | -exp_cov auto -cov_cutoff auto | Kmer length of 51 was used |
| GapFiller | [64] | v1-11 | -o 10 -m 55 | |
| clc_bio | program used: clc_mapper | 4.1.0 | -l 0.9 -s 0.9 | |
| BLAST | [67] | 2.25 | default | |
| CEGMA | [39] | 2.0 | default | |
| SNAP | [76] | 2006-07-28 | default | used within MAKER pipeline |
| GeneMark | [77] | v.2.3e | –BP OFF -max_nnn 500 -min_contig 10000 | |
| MAKER2 | [41] | 2.25 | default | maker_opts file changed |
| Augustus | [42] | 2.7 | script used: auto_Aug.pl | |
| orthoMCL | [46] | 2.0.3 | default | |
| MUSCLE | [78] | 3.8.31 | default | |
| RAxML | [68] | 7.6.4 | -m GTRGAMMA | |
| MrBayes | [69] | 3.2 | lset nst = 6 rates = gamma | |
| PhyloBayes | [70] | 2.3 | -cat -gtr | |
| FigTree | [72] | 3.0.2 | used in construction of Figure 3 C and Figure 4 | |
| iTOL | [71] | used in construction of Figure 3 C and Figure 4 | ||
| Geneious | www.geneious.com | R7 | used for construction of Figure 3 A, B |
* Unless otherwise specified, default parameters were used.