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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