Effects of sequence alignment procedures on estimates of phylogeny

[1]  J. Felsenstein,et al.  A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.

[2]  J. Huelsenbeck Performance of Phylogenetic Methods in Simulation , 1995 .

[3]  J. Hein Unified approach to alignment and phylogenies. , 1990, Methods in enzymology.

[4]  N. Goldman,et al.  Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. , 1994, Molecular biology and evolution.

[5]  R. Dores,et al.  Obtaining a more resolute teleost growth hormone phylogeny by the introduction of gaps in sequence alignment. , 1995, Molecular phylogenetics and evolution.

[6]  D. Penny Towards a basis for classification: the incompleteness of distance measures, incompatibility analysis and phenetic classification. , 1982, Journal of theoretical biology.

[7]  H Kishino,et al.  Freeing phylogenies from artifacts of alignment. , 1992, Molecular biology and evolution.

[8]  Nick Goldman,et al.  MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES , 1990 .

[9]  B. Rannala,et al.  Phylogenetic methods come of age: testing hypotheses in an evolutionary context. , 1997, Science.

[10]  D A Morrison,et al.  Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa. , 1997, Molecular biology and evolution.

[11]  G A Churchill,et al.  Estimation and reliability of molecular sequence alignments. , 1995, Biometrics.

[12]  J A Lake,et al.  The order of sequence alignment can bias the selection of tree topology. , 1991, Molecular biology and evolution.

[13]  J. Felsenstein Phylogenies from molecular sequences: inference and reliability. , 1988, Annual review of genetics.

[14]  J. Felsenstein CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[15]  Nick Goldman,et al.  MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM , 1995 .

[16]  M S Waterman,et al.  Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.

[17]  Masami Hasegawa,et al.  CONFIDENCE LIMITS ON THE MAXIMUM‐LIKELIHOOD ESTIMATE OF THE HOMINOID TREE FROM MITOCHONDRIAL‐DNA SEQUENCES , 1989, Evolution; international journal of organic evolution.