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sequences with insertions. Proc Natl Acad Sci
USA 102:10557-10562
7. Larkin M, Blackshields G, Brown N, Chenna R,
McGettigan P, McWilliam H, Valentin F, Wal-
lace I, Wilm A, Lopez R, Thompson J, Gibson
T, Higgins D (2007) Clustal W and Clustal X
version 2.0. Bioinformatics 23:2947-2948
8. Edgar R (2004) MUSCLE: multiple sequence
alignment with high accuracy and high
throughput. Nucleic Acids Res 32:1792-1797
9. Liu K, Raghavan S, Nelesen S, Linder C, War-
now T (2009) Rapid and accurate large-scale
coestimation of sequence alignments and phy-
logenetic trees. Science 324:1561-1564
10. Fletcher W, Yang Z (2010) The effect of inser-
tions, deletions, and alignment errors on the
branch-site test of positive selection. Mol Biol
Evol 27:2257-2267
11. Jordan G, Goldman N (2012) The effects of
alignment error and alignment filtering on the
sitewise detection of positive selection. Mol
Biol Evol 29:1125-1139
12. Dessimoz C, Gil M (2010) Phylogenetic
assessment of alignments reveals neglected
tree signal in gaps. Genome Biol 11:R37
13. Landan G, Graur D (2007) Heads or tails: a
simple reliability check for multiple sequence
alignments. Mol Biol Evol 24:1380-1383
14. Suchard M, Redelings B (2006) BAli-Phy:
simultaneous Bayesian inference of alignment
and phylogeny. Bioinformatics 22:2047-2048
15. Nov ´ k A, Mikl ´ s I, Lyngsø R, Hein J (2008)
StatAlign: an extendable software package for
joint Bayesian estimation of alignments and
evolutionary
trees.
Bioinformatics
24:2403-2404
16. L ¨ ytynoja A, Vilella A, Goldman N (2012)
Accurate extension of multiple sequence align-
ments using a phylogeny-aware graph algo-
rithm. Bioinformatics 28:1684-1691
17. L¨ytynoja A, Goldman N (2010) webPRANK:
a phylogeny-aware multiple sequence aligner
with interactive alignment browser. BMC Bio-
informatics 11:579
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