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Table 2 Running time and average SPS with genome MSA

From: HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing

  Φ DNA (1 ×) Φ DNA (100 ×) Φ DNA (1000 ×)
Time Memory Avg SPS Time Memory (GB) Avg SPS Time Memory (GB) Avg SPS
MUSCLE 45 m 23 s ~ 8 GB 0.951 – – – – – –
MAFFT 1 m 20 s ~ 100 MB 0.926 13 m 21 s ~ 8 0.926 – – –
Clustal-Omega 1 h 25 m ~ 3 GB 0.913 15 h 56 m ~ 30 0.913 – – –
HAlign 2 m 12 s ~ 300 MB 0.722 26 m 35 s ~ 8 0.722 5 h 28 m ~ 40 0.722
HAlign-II 14 s ~ 100 MB 0.723 10 m 24 s ~ 2 0.723 1 h 25 m ~ 15 0.723
  1. Memory is the maximum memory usage (the same as below)
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Algorithms for Molecular Biology

ISSN: 1748-7188