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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)