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Table 4 Running time and average SPS with protein MSA

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

  Φ Protein (1 ×) Φ Protein (100 ×) Φ Protein (1000 ×)
Time Memory (MB) Avg SPS Time Memory (GB) Avg SPS Time Memory (GB) Avg SPS
MUSCLE 3 m 13 s ~ 300 0.892 ~ 34 h ~ 10 0.892 – – –
MAFFT 5 m 53 s ~ 100 0.878 37 m 51 s ~ 5 0.878 7 h 22 m ~ 30 0.878
Clustal-Omega 54 m 08 s ~ 100 0.912 28 h 15 m ~ 5 0.912 – – –
SparkSW 3 m 23 s ~ 100 0.716 1 h 12 m ~ 2 0.716 5 h 30 m ~ 18 0.716
HAlign-II 1 m 45 s ~ 100 0.695 26 m 36 s ~ 1 0.695 2 h 52 m ~ 10 0.695
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Algorithms for Molecular Biology

ISSN: 1748-7188