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Table 1 Alignment time comparison of various numbers of human mtDNA genomes (complete sequences)

From: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

 

No. of sequences compared

Method

50

100

200

400

MISHIMA + MAFFT

00:01:05

00:02:23

00:12:59

01:38:09

MISHIMA + CLUSTAL W -max-depth = 1

00:00:43

00:02:06

00:06:05

00:34:19

CLUSTAL W

02:15:32

04:48:59

10:16:22

25:08:23

MUSCLE

00:44:29

01:28:12

02:08:44

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MAFFT

00:02:43

00:05:44

00:16:31

00:38:51

Nucleotide diversity

0.003

0.002

0.002

0.002