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Table 1 Alignment methods and parameters used in this study.

From: Automatic extraction of reliable regions from multiple sequence alignments

Method Description/Options
Poa [17,18] local unprogressive mode using blosum80.mat
ClustalW version 1.83 [19] default parameters
Muscle version 3.52 [15] one iteration: -stable -maxiters 1
two iterations: -stable -maxiters 2
default: -stable
Probcons version 1.09 [2] default parameters
Dialign version 2.2 [20,21] default parameters
Mafft version 5.63 [3,22] -localpair
-localpair -maxiterate 100
-globalpair
-globalpair -maxiterate 100
Kalign [4] default parameters