HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

Bioinformatics

Volumn 28, Issue 8, 2012, Pages 1170-1171

  Westesson, Oscar ^a   Barquist, Lars ^b   Holmes, Ian ^a  

^a University of California at Berkeley   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 120; GP120 PROTEIN, SIMIAN IMMUNODEFICIENCY VIRUS; MEMBRANE PROTEIN; VIRUS ENVELOPE PROTEIN;

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS; INDEL MUTATION; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; SEQUENCE ALIGNMENT; SIMIAN IMMUNODEFICIENCY VIRUS;

BAYES THEOREM; HIV; HIV ENVELOPE PROTEIN GP120; INDEL MUTATION; MARKOV CHAINS; MEMBRANE GLYCOPROTEINS; MONTE CARLO METHOD; PHYLOGENY; SEQUENCE ALIGNMENT; SIMIAN IMMUNODEFICIENCY VIRUS; SOFTWARE; VIRAL ENVELOPE PROTEINS;

EID: 84859784475     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts058     Document Type: Article

References (5)

1. Bouchard-Côté, A. et al. (2009) Efficient inference in phylogenetic InDel trees. In Advances in Neural Information Processing Systems 21 (NIPS), Vancouver, Canada.
2. Holmes, I. and Bruno, W.J. (2001) Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics, 17, 803-820.
3. Leonard, C. et al. (1990) Assignment of intrachain disulfide bonds and characterization of potential glycosylation sites of the type 1 recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells. J. of Biol. Chem., 265, 10373.
4. Miklós, I. et al. (2004) A long indel model for evolutionary sequence alignment. Mol. Biol. Evol., 21, 529-540.
5. Redelings, B.D. and Suchard, M.A. (2005) Joint Bayesian estimation of alignment and phylogeny. Systematic Biol., 54, 401-418.