Literature

Authors	Year	Title
J. Hein	1989	A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given
J. Hein	1989	A tree reconstruction method that is economical in the number of pairwise comparisons used
T. Jiang, Lawler, E. L., Wang, A.	1994	Aligning sequences via an evolutionary tree: complexity and approximation
O. Gotoh	1982	An improved algorithm for matching biological sequences
M. A. Larkin, Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G.	2007	Clustal W and Clustal X version 2.0
W. Wheeler	1999	Fixed character states and the optimization of molecular sequence data
W. C. Wheeler	2003	Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search
D. A. Morrison	2006	Multiple sequence alignment for phylogenetic purposes
D. R. Frost, Rodrigues, M. T., Grant, T., Titus, T. A.	2001	Phylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology
A. Löytynoja, Goldman N.	2008	Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
W. C. Wheeler	1995	Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
S. Schulmeister, Wheeler, W. C., Carpenter, J. M.	2002	Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
J. D. Thompson, Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G.	1997	The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
B. Schwikowski, Vingron M.	1997	The deferred path heuristic for the generalized tree alignment problem