Table 1 Genome aligner version and parameters

MUMmer

3.22

’nucmer’ (parameters’–maxgap = 500 –coords’); delta-filter (options’-q -r -o 0’) and’show-aligns’.

MGA

mgadist-2003-03-18

’mkvtree’ (parameters’-dna -lcp -suf -tis -indexname’) and’mga.128seqs’ (parameters’-l 50 20 -gl 3000 -always –clustalw)’

LAGAN

1.1

with default parameters

MAUVE

2.3.1

with default parameters except for’–weight = 5000’ and’–output-alignment’ for XMFA file output

ProgressiveMAUVE

2.3.1

with default parameters except for’–output-alignment’ option for XMFA file output

YOC

1.0

with default parameters : for ‘YASS’ (parameter ‘E-value threshold’: 10) and for Overlap Chainer (parameter ‘overlap ratio’ : 10%).