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consistency-based multiple sequence alignment.
Genome Res 15:330-340
11. Edgar RC (2004) MUSCLE: multiple sequence
alignment with high accuracy and high
throughput. Nucleic Acids Res 32:1792-1797
12. Katoh K, Misawa K, Kuma K, Miyata T (2002)
MAFFT: a novel method for rapid multiple
sequence alignment based on fast Fourier
transform. Nucleic Acids Res 30:3059-3066
13. Katoh K, Kuma K, Toh H, Miyata T (2005)
MAFFT version 5: improvement in accuracy of
multiple sequence alignment. Nucleic Acids
Res 33:511-518
14. Katoh K, Toh H (2008) Recent developments
in the MAFFT multiple sequence alignment
program. Brief Bioinform 9:286-298
15. Pei J, Grishin NV (2006) MUMMALS: multi-
ple sequence alignment improved by using
hidden Markov models with local structural
information. Nucleic Acids Res 34:4364-4374
16. Paten B, Herrero J, Beal K, Birney E (2009)
Sequence progressive alignment, a framework
for practical large-scale probabilistic consis-
tency alignment. Bioinformatics 25:295-301
17. Subramanian AR, Kaufmann M, Morgenstern
B (2008) DIALIGN-TX: greedy and progres-
sive approaches for segment-based multiple
sequence alignment. Algorithms Mol Biol 3:6
18. Schwartz AS, Pachter L (2007) Multiple
alignment by sequence annealing. Bioinfor-
matics 23:e24-e29
19. Bradley RK, Roberts A, Smoot M, Juvekar S,
Do J, Dewey C, Holmes I, Pachter L (2009)
Fast statistical alignment. PLoS Comput Biol
5:e1000392
20. Sahraeian SM, Yoon BJ (2010) PicXAA: greedy
probabilistic construction of maximum
expected accuracy alignment of multiple
Sequences. Nucleic Acids Res 38:4917-4928
21. Roshan U, Livesay DR (2006) Probalign:
multiple sequence alignment using partition
function posterior probabilities. Bioinformatics
22:2715-2721
22. Gonnet GH, Cohen MA, Benner SA (1992)
Exhaustive matching of the entire protein
sequence database. Science 256:1443-1445
23. Sahraeian SM, Yoon BJ (2010) PicXAA-R:
efficient structural alignment of multiple RNA
sequences using a greedy approach. BMC Bio-
informatics 11(Suppl 1):S38
24. Sahraeian SM, Yoon BJ (2011) PicXAA-Web:
a web-based platform for non-progressive max-
imum expected accuracy alignment of multiple
biological sequences. Nucleic Acids Res 39:
W8-W12
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