Table 1 Multiple sequence alignment programs used in this study

CLUSTALW v2.0.10

http://www.clustal.org/download/current/

Progressive

CLUSTAL O. v1.2.0

http://www.clustal.org/omega

Hidden Markov Model

DIALIGN-TX v1.0.2

http://dialign-tx.gobics.de/download

Consistency

MAFFT v6.714b

http://mafft.cbrc.jp/alignment/software/

Fast Fourier T./Iterative/Consistency

MUSCLE v3.8.31

http://www.drive5.com/muscle/downloads.htm

Iterative

POA v2

http://sourceforge.net/projects/poamsa

Graphs

Probalign v1.4

http://cs.njit.edu/usman/probalign/

Partition Function/Consistency

Probcons v1.12

http://probcons.stanford.edu/download.html

Hidden Markov Model/Consistency

T-Coffee v8.99

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

Consistency (multi-core usage capable)