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	title = {Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites},
	journal = {Molecular Biology and Evolution},
	volume = {10},
	number = {6},
	year = {1993},
	note = {PDF},
	pages = {1396-1401},
	keywords = {gamma distribution, ML, phylogenetics, rates, substitution rates},
	author = {Yang, Ziheng}
}
@article {7848,
	title = {Investigation of molluscan phylogeny on the basis of 18S rRNA sequences},
	journal = {Molecular Biology and Evolution},
	volume = {13},
	number = {10},
	year = {1996},
	pages = {1306-1317},
	keywords = {18S, molecules, mollusca, phylogeny},
	author = {Winnepenninckx, Birgitta}
}
@article {7771,
	title = {Substitution-rate variation among sites and the estimation of transition bias},
	journal = {Molecular Biology and Evolution},
	volume = {11},
	year = {1993},
	note = {DO NOT HAVE},
	pages = {426{\textendash}442},
	keywords = {phylogenetics, ts-tv bias},
	author = {Wakeley, J.}
}
@article {7599,
	title = {Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences},
	journal = {Molecular Biology and Evolution},
	volume = {16},
	number = {5},
	year = {1999},
	note = {PDF},
	pages = {590{\textendash}601},
	keywords = {likelihood, ML, rates},
	author = {Takezaki, Naoko and Gojobori, Takashi}
}
@article {7602,
	title = {Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees},
	journal = {Molecular Biology and Evolution},
	volume = {10},
	year = {1993},
	note = {PDF},
	pages = {512-526},
	keywords = {ML, molecular characters, phylogenetics},
	author = {Tamura, K. and Nei, M.}
}
@article {7581,
	title = {Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {6},
	year = {2005},
	note = {PDF},
	pages = {1386{\textendash}1392},
	keywords = {likelihood, ML, model selection, optimization, phylogenetics},
	author = {Sullivan, Jack and Abdo, Zaid and Joyce, Paul and Swofford, David L.}
}
@article {7519,
	title = {Likelihood, parsimony, and heterogeneous evolution},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {5},
	year = {2005},
	note = {PDF},
	pages = {1161-1164},
	keywords = {heterotachy, ML, parsimony, phylogenetics, rates},
	author = {Spencer, Matthew and Susko, Edward and Roger, Andrew J.}
}
@article {7361,
	title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
	journal = {Molecular Biology and Evolution},
	volume = {4},
	number = {4},
	year = {1987},
	note = {PDF},
	pages = {406-425},
	keywords = {molecular characters, neighbor-joining},
	author = {Saitou, Naruya and Nei, Masatoshi}
}
@article {7356,
	title = {A simple method for estimating and testing minimum-evolution trees},
	journal = {Molecular Biology and Evolution},
	volume = {9},
	year = {1992},
	note = {DO NOT HAVE},
	pages = {945{\textendash}967},
	keywords = {minimum evolution, phylogenetics},
	author = {Rzhetsky, A. and Nei, M.}
}
@article {7180,
	title = {A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting},
	journal = {Molecular Biology and Evolution},
	volume = {13},
	number = {9},
	year = {1996},
	note = {PDF},
	pages = {1174-1186},
	keywords = {homoplasy, morphological characters, phylogenetics, weighting},
	author = {Philippe, Harv{\'e} and Lecointre, Guillaume and L{\^e}, Hoc Lanh V{\^a}n and Guyader, Harv{\'e} Le}
}
@article {7022,
	title = {Methods for inferring phylogenies from nucleotide acid sequence data by using maximum likelihood and linear invariants},
	journal = {Molecular Biology and Evolution},
	volume = {8},
	year = {1991},
	note = {DO NOT HAVE},
	pages = {128-143},
	author = {Navidi, W. C. and Churchill, G. A. and Haeseler, A. von}
}
@article {6800,
	title = {Recovering evolutionary trees under a more realistic model of sequence evolution},
	journal = {Molecular Biology and Evolution},
	volume = {11},
	number = {4},
	year = {1994},
	note = {PDF},
	pages = {605-612},
	keywords = {bias, LogDet, ML, molecular characters, phylogenetics},
	author = {Lockhart, Peter J. and Steel, Michael A. and Hendy, Michael D. and Penny, David}
}
@article {6713,
	title = {A simulation comparison of phylogeny algorithms under equaland unequal evolutionary rates},
	journal = {Molecular Biology and Evolution},
	volume = {11},
	year = {1994},
	note = {DO NOT HAVE},
	pages = {459{\textendash}468},
	keywords = {phylogenetics},
	author = {Kuhner, M. K. and Felsenstein, Joseph}
}
@article {6495,
	title = {A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given},
	journal = {Molecular Biology and Evolution},
	volume = {6},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {649{\textendash}668},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Hein, J.}
}
@article {6496,
	title = {A tree reconstruction method that is economical in the number of pairwise comparisons used},
	journal = {Molecular Biology and Evolution},
	volume = {6},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {669{\textendash}684},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Hein, J.}
}
@article {6417,
	title = {Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites},
	journal = {Molecular Biology and Evolution},
	volume = {12},
	year = {1995},
	note = {DO NOT HAVE},
	pages = {546{\textendash}557},
	keywords = {invariants, ML, phylogenetics},
	author = {Gu, X.}
}
@article {6282,
	title = {18S ribosomal RNA gene phylogeny for some Rhabditidae related to <i>Caenorhabditis</i>},
	journal = {Molecular Biology and Evolution},
	volume = {12},
	number = {2},
	year = {1995},
	note = {PDF},
	pages = {346-358},
	keywords = {18S, caenorhabditis, nematoda, phylogeny, rDNA},
	author = {Fitch, David H. A. and Bugaj-Gaweda, Bozena and Emmons, Scott W.}
}
@article {6169,
	title = {Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis},
	journal = {Molecular Biology and Evolution},
	volume = {10},
	number = {1},
	year = {1993},
	note = {PDF},
	pages = {256-267},
	keywords = {28S, molecules, phylogenetics, rDNA, secondary structure},
	author = {Dixon, Michael T. and Hillis, David M.}
}
@article {6120,
	title = {When does the incongruence length difference test fail?},
	journal = {Molecular Biology and Evolution},
	volume = {19},
	number = {4},
	year = {2002},
	note = {DO NOT HAVE},
	pages = {432-437},
	keywords = {ild, phylogenetics},
	author = {Darlu, P. and Lecointre, G.}
}
@article {6088,
	title = {Sampling properties of DNA sequence data in phylogenetic analysis},
	journal = {Molecular Biology and Evolution},
	volume = {12},
	year = {1995},
	note = {DO NOT HAVE},
	pages = {814-822},
	author = {Cummings, M. P. and Otto, S. P. and Wakeley, J.}
}
@article {6089,
	title = {Can three incongruence tests predict when data should be combined?},
	journal = {Molecular Biology and Evolution},
	volume = {14},
	number = {7},
	year = {1997},
	note = {PDF},
	pages = {733-740},
	keywords = {combined data analyses, ild, incongruence, phylogenetics, templeton test, total evidence},
	author = {Cunningham, Clifford W.}
}
@article {6040,
	title = {Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference},
	journal = {Molecular Biology and Evolution},
	volume = {18},
	number = {6},
	year = {2001},
	note = {PDF},
	pages = {1024-1033},
	keywords = {bias, LogDet, molecular characters, parsimony, phylogenetics},
	author = {Conant, Gavin C. and Lewis, Paul O.}
}
@article {5708,
	title = {A molecular phylogeny of the bivalve mollusks},
	journal = {Molecular Biology and Evolution},
	volume = {14},
	number = {6},
	year = {1997},
	note = {PDF},
	pages = {619-629},
	keywords = {18S, atrina, bivalvia, molecular characters, mollusca, phylogeny, Pteria},
	author = {Adamkewicz, S. Laura and Harasewych, M. G. and Blake, Judith and Saudek, Deborah and Bult, Carol J.}
}
@article {938,
	title = {A molecular phylogeny of the bivalve mollusks},
	journal = {Molecular Biology and Evolution},
	volume = {14},
	number = {6},
	year = {1997},
	pages = {619-629},
	keywords = {18S, atrina, bivalvia, mollusca, phylogeny, Pteria},
	author = {Adamkewicz, S. Laura and Harasewych, M. G. and Blake, Judith and Saudek, Deborah, Bult, Carol J.}
}
@article {1689,
	title = {Investigation of molluscan phylogeny on the basis of 18S rRNA sequences},
	journal = {Molecular Biology and Evolution},
	volume = {13},
	number = {10},
	year = {1996},
	pages = {1306-1317},
	keywords = {18S, molecules, mollusca, phylogeny},
	author = {Winnepenninckx, Birgitta}
}
