Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups
Calculation benchmark made on a workstation equipped with a 3.2 GHz Intel i7 -970 processor (6 cores with hyper-threading, i.e., 12 simultaneous threads). A. The Gegenees source code was modified so that the number of simultaneous threads was limited to 1, 2, 3…. The time for completing a comparison with 10 Bacillus.spp genomes (∼5 Mb each) with BLAST (blastall) or BLAST+ was measured. When no thread limit was used Gegenees chose to use 12 threads on this machine. B. Time required for completing an alignment with an increasing number of Bacillus spp. genomes. Progressive Mauve (version 2.3.1) with default settings and Gegenees with different settings (500/500 or 200/100 using blastall or BLAST+) were compared. The asterisk indicates the upper limit of genomes (30) we could align in Progressive Mauve on this machine.