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Table 2 Results on technical criteria investigated in a comparative study on PRRSV sequence alignment algorithmsa

From: Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)

Criterion Algorithm
Clustal W MAFFT T-Coffee Muscle Clustal 0mega 
1. Handling capability of large dataset: capacity to generate results in less than 2 weeks (yes/no)
 10 replicates of 238 sequences yes yes yes yes yes
 5 replicates of 476 sequences yes yes yes yes yes
 2 replicates of 1191 sequences yes yes yes yes yes
 Full dataset (2383 sequences) no yes no yes yes
2. Rapidity: average time (minutes) necessary to align (Linux platform, 10 physical cores)
 10 replicates of 238 sequences 12.8 0.2 13.1 0.2 0.2
 5 replicates of 476 sequences 57.1 1.0 56.1 0.7 0.4
 2 replicates of 1191 sequences 1040.5 7.0 540.0 3.9 1.2
 Full dataset (2383 sequences) n/a 28.5 n/a 17.0 2.9
3. Multiplatform availability (yes/no)
 Web, Windows and Linux yes yes yes yes yes
4. Management of IUB ambiguity symbol characters: ability to manage symbols other than A, T, C and G
 List of managed symbols N N, R, Y, W,
S, K, M, D,
V, H, B
N, R, Y, W,
S, K, M, D,
V, H, B
N, R, Y N
  1. aThe open gap penalties used was 30 for Clustal W, 7 for MAFFT, −200 for T-Coffee, −1000 for Muscle and default for Clustal Omega. The dataset included 2383 sequences collected in 2010–2014