Literature

Authors	Year	Title
H. Philippe, Lecointre, G., Lê, H. Lanh Vân, Le Guyader, H.	1996	A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting
J. Hein	1989	A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given
A. Rzhetsky, Nei M.	1992	A simple method for estimating and testing minimum-evolution trees
M. K. Kuhner, Felsenstein J.	1994	A simulation comparison of phylogeny algorithms under equaland unequal evolutionary rates
J. Hein	1989	A tree reconstruction method that is economical in the number of pairwise comparisons used
C. W. Cunningham	1997	Can three incongruence tests predict when data should be combined?
G. C. Conant, Lewis P. O.	2001	Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference
K. Tamura, Nei M.	1993	Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
J. Sullivan, Abdo, Z., Joyce, P., Swofford, D. L.	2005	Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation
M. Spencer, Susko, E., Roger, A. J.	2005	Likelihood, parsimony, and heterogeneous evolution
X. Gu	1995	Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
Z. Yang	1993	Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
P. J. Lockhart, Steel, M. A., Hendy, M. D., Penny, D.	1994	Recovering evolutionary trees under a more realistic model of sequence evolution
M. T. Dixon, Hillis D. M.	1993	Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis
J. Wakeley	1993	Substitution-rate variation among sites and the estimation of transition bias
P. Darlu, Lecointre G.	2002	When does the incongruence length difference test fail?