Table 9

Average running time (in seconds) per multiple alignment for the 180 sequence families of IRMBASE and for 141 sequence families in BAliBASE 2.1. Program runs were performed on a Linux workstation (RedHat 8.0) with an 3.2 GHz Pentium 4 processor and 2 GB Ram.

Method

Average runtime on IRMBASE 1.0

Average runtime on BAliBASE 2.1

DIALIGN-T

2.36

1.38

DIALIGN 2.2

3.33

1.30

T-COFFEE 1.37

27.54

7.64

PROBCONS 1.09

12.37

2.66

POA V2

1.44

0.58

MUSCLE 3.5

9.37

0.60

CLUSTAL W 1.83

1.41

0.47

Subramanian et al. BMC Bioinformatics 2005 6:66   doi:10.1186/1471-2105-6-66