Accelerated large-scale multiple sequence alignment

BMC Bioinformatics

Table 2 Comparison of MUSCLE and MUDISC alignment quality

Reference Set	MUSCLE Avg. Score	P-value, Rank	MUDISC (near) Avg. Score	P-value, Rank	MUDISC (nearest) Avg. Score
BRAliBase k7	0.6846	1.42e-4, >	0.6851	0.875, >	0.6839
BRAliBase k15	0.6914	1.18e-3, >	0.6819	0.285, <	0.6814
MDSA BAliBASE	0.3125	9.58e-9, <	0.3623	0.806, <	0.3629
MDSA SMART	0.6195	7.46e-3, <	0.6295	0.830, >	0.6316

The average quality scores for MUSCLE and MUDISC are shown on four reference sets. BRAliScore is reported for BRAliBase, and Q score is reported for MDSA. A variant of MUDISC that uses the nearest neighbor search method is also shown. The P-values from a Friedman rank test indicate the difference between two adjacent programs, and the relational symbols indicate which program ranked higher.

ISSN: 1471-2105