Biology Reference
In-Depth Information
3. Edgar RC (2010) Quality measures for protein
alignment benchmarks. Nucleic Acids Res
38(7):2145-2153
4. Thompson JD, Linard B, Lecompte O, Poch O
(2011) A comprehensive benchmark study of
multiple sequence alignment methods: current
challenges and future perspectives. PLoS One
6(3):e18093
5. L¨ytynoja A (2012) Alignment methods: stra-
tegies, challenges, benchmarking, and compara-
tive overview. Methods Mol Biol 855:203-235
6. Thompson JD, Higgins DG, Gibson TJ
(1994) CLUSTALW: improving the sensitivity
of progressive multiple sequence alignment
through sequence weighting, position-specific
gap penalties and weight matrix choice.
Nucleic Acids Res 22(22):4673-4680
7. Morrison DA (2009) Why would phylogeneti-
cists ignore computerized sequence alignment?
Syst Biol 58(1):150-158
8. Mardis ER (2008) The impact of next-
generation sequencing technology on genetics.
Trends Genet 24(3):133-141. doi: 10.1016/
j.tig.2007.12.007
9. Anisimova M, Cannarozzi G, Liberles D
(2010) Finding the balance between the math-
ematical and biological optima in multiple
sequence alignment. Trends Evol Biol 2(1):e7
10. Stebbings LA, Mizuguchi K (2004) HOM-
STRAD: recent developments of the Homolo-
gous Protein Structure Alignment Database.
Nucleic Acids Res
domain constraints. Mol Biol Evol 29(9):
2133-2145
18. Dalquen DA, Anisimova M, Gonnet GH, Des-
simoz C (2012) ALF-a simulation framework
for genome evolution. Mol Biol Evol 29(4):
1115-1123
19. Thompson JD, Plewniak F, Poch O (1999)
A comprehensive comparison of multiple
sequence alignment programs. Nucleic Acids
Res 27(13):2682-2690, gkc432 [pii]
20. Blackburne BP, Whelan S (2012) Measuring
the distance between multiple sequence align-
ments. Bioinformatics 28(4):495-502. doi:
10.1093/bioinformatics/btr701
21. L ¨ ytynoja A, Goldman N (2008) Phylogeny-
aware gap placement prevents errors in
sequence alignment and evolutionary analysis.
Science 320(5883):1632-1635. doi: 10.1126/
science.1158395
22. Golubchik T, Wise MJ, Easteal S, Jermiin LS
(2007) Mind the gaps: evidence of bias in esti-
mates of multiple sequence alignments. Mol
Biol Evol 24(11):2433-2442
23. Huelsenbeck JP (1995) Performance of phylo-
genetic methods in simulation. Syst Biol 44(1):
17-48
24. Do CB, Mahabhashyam MS, Brudno M,
Batzoglou S (2005) ProbCons: probabilistic
consistency-based multiple sequence align-
ment.
Genome
Res
15(2):330-340.
doi: 10.1101/gr.2821705
25. Notredame C, Higgins DG, Heringa J (2000)
T-Coffee: a novel method for fast and accurate
multiple sequence alignment. J Mol Biol 302
(1):205-217. doi: 10.1006/jmbi.2000.4042
26. Lassmann T, Sonnhammer ELL (2005) Auto-
matic assessment of alignment quality. Nucleic
Acids Res 33(22):7120-7128
27. Landan G, Graur D (2007) Heads or tails: a
simple reliability check for multiple sequence
alignments. Mol Biol Evol 24(6):1380-1383
28. Hall BG (2008) How well does the HoT score
reflect sequence alignment accuracy? Mol Biol
Evol 25(8):1576-1580
29. Chothia C, Lesk AM (1986) The relation
between the divergence of sequence and struc-
ture in proteins. EMBO J 5(4):823
30. Mizuguchi K, Deane CM, Blundell TL, Over-
ington JP (1998) HOMSTRAD: a database of
protein structure alignments for homologous
families. Protein Sci 7(11):2469-2471.
doi: 10.1002/pro.5560071126
31. Thompson JD, Plewniak F, Poch O (1999)
BAliBASE: a benchmark alignment database for
the evaluation of multiple alignment programs.
Bioinformatics 15(1):87-88, btc017 [pii]
32(Database
issue):
D203-D207
11. Thompson JD, Koehl P, Ripp R, Poch O
(2005) BAliBASE 3.0: latest developments of
the multiple sequence alignment benchmark.
Proteins 61:127-136
12. Stoye J, Evers D, Meyer F (1998) Rose: gen-
erating
sequence
families. Bioinformatics
14(2):157-163
13. Cartwright RA (2005) DNA assembly with
gaps (Dawg): simulating sequence evolution.
Bioinformatics 21(Suppl 3):iii31-iii38
14. Hall BG (2008) Simulating DNA coding
sequence evolution with EvolveAGene 3. Mol
Biol Evol 25(4):688-695
15. Fletcher W, Yang Z (2009) INDELible: a flexi-
ble simulator of biological sequence evolution.
Mol Biol Evol 26(8):1879-1888
16. Sipos B, Massingham T, Jordan GE, Goldman
N (2011) PhyloSim - Monte Carlo simulation
of sequence evolution in the R statistical com-
puting environment. BMC Bioinformatics
12(1):104
17. Koestler T, Av H, Ebersberger I (2012)
REvolver: modeling sequence evolution under
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