Literature

Authors	Year	Title
H. Kishino, Miyata, T., Hasegawa, M.	1990	Maximum likelihood inference of protein phylogeny and the origin of chloroplasts., J. Mol. Evol., 30, 151-160.
A. G. Kluge, Farris J.	1969	Quantitative phyletics and the evolution of anurans
A. Knight, Mindell D. P.	1993	Substitution bias weighting of DNA sequence evolution and the phylogenetic position of Fea's viper
B. Kolaczkowski, Thornton J. W.	2004	Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
F. Krauss	1988	An empirical evaluation of the use of the ontogenetic polarization criterion in phylogenetic inference
M. K. Kuhner, Felsenstein J.	1994	A simulation comparison of phylogeny algorithms under equaland unequal evolutionary rates
M. Källersjö, Albert, V. A., Farris, J. S.	1999	Homoplasy increases phylogenetic structure
M. Källersjö, Farris, J. S., Kluge, A. G., Bult, C.	1992	Skewness and permutation
J. De Laet	2005	Parsimony and the problem of inapplicables in sequence data
J. De Laet, Smets E.	1998	On the three taxon approach to parsimony analysis
C. Lanave, Preparata, , G., Saccone, C., Serio, G.	1984	A new method for calculating evolutionary substitution rates
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
G. Lecointre, Deleporte P.	2004	Total evidence requires exclusion of phylogenetically misleading data
F. Legendre, Whiting, M. F., Bordereau, C., Cancello, Eliana, M., Evans, T. A., Grandcolas, P.	2008	The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors
P. O. Lewis	2001	Phylogenetic systematics turns over a new leaf
P. O. Lewis	2001	A likelihood approach to estimating phylogeny from discrete morphological character data
P. O. Lewis	1998	Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
P. J. Lockhart, Steel, M. A., Hendy, M. D., Penny, D.	1994	Recovering evolutionary trees under a more realistic model of sequence evolution
J. B. Losos, Glor R. E.	2003	Phylogenetic comparative methods and the geography of speciation
J. B. Losos, Ricklefs R. E.	2009	Adaptation and diversification on islands
A. Löytynoja, Goldman N.	2008	Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
C. Lydeard, Holznagel, W. E., Schnare, M. N., Gutell, R. R.	2000	Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures
D. R. Maddison, Swofford, D. L., Maddison, W. P.	1997	NEXUS: an extensible file format for systematic information
L. P. Maia, Colato, A., Fontanari, J. !eF.	2004	Effect of selection on the topology of genealogical trees
J. G. Maisey, Naylor, G. J. P., Ward, David, J.	2004	Mesozoic elasmobranchs, neoselchian phylogeny and the rise of modern elasmobranch diversity
V. Makarenkov, Legendre, P., Desdevises, Y.	2004	Modelling phylogenetic relationships using reticulated networks
E. P. Martins, Hansen T. F.	1997	Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data
M. Matsumoto	2003	Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences
M. Matsumoto	2003	Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences
C. P. Meyer	2003	Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics
C. P. Meyer, Geller, J. B., Paulay, G.	2005	Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods
D. P. Mindell, Honeycutt R. L.	1990	Ribosomal RNA in vertebrates: evolution and phylogenetic applications
A. Ø. Mooers	2007	The diversity of biodiversity
D. A. Morrison	2006	Multiple sequence alignment for phylogenetic purposes
S. Nee	2001	Inferring speciation rates from phylogenies
M. Nei, Kumar S.	2000	Molecular evolution and phylogenetics
K. C. Nixon	Submitted	WinClada ver. 1.0000
K. C. Nixon	1999	The parsimony ratchet, a new method for rapid parsimony analysis
K. C. Nixon, Carpenter J. M.	1993	On outgroups
M. A. Norell, Novacek M. J.	1992	The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history
R. D. M. Page, Holmes E. C.	1998	Molecular evolution: a phylogenetic approach
M. Pagel	1999	The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies
M. Pagel	1999	Inferring the historical patterns of biological evolution
M. Pagel	1997	Inferring evolutionary processes from phylogenies
M. Pagel	1994	Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters
Y. I. Pavlinov	1998	K problemeaksiomaticheskogo obosnovaniya evolyutsionnoj kladistiki
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
H. Philippe, Sörhannus, U., Baroin, A., Perasso, R., Gasse, F., Adoutte, A.	1995	Comparison of molecular and paleontological data in doatoms suggests a major gap in the fossil record
D. Pol, Norell M. A.	2001	Comments on the manhattan stratigraphic measure
D. Posada, Buckley T. R.	2004	Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests

Authors