The relative performance of Bayesian and parsimony approaches when Sampling Characters . . .

DMCA

The relative performance of Bayesian and parsimony approaches when Sampling Characters . . . (2006)

Cached

Download Links

[www.calacademy.org]

by Mark P. Simmons , Li-Bing Zhang , Colleen T. Webb , Aaron Reeves , Jeremy A. Miller

Citations:

3 - 0 self

Citations

5088	Paup∗ . Phylogenetic analysis using parsimony ( ∗ and other methods - Swofford - 1998
4630	A new look at the statistical model identification - Akaike - 1974
3989	Confidence limits on phylogenies: an approach using the bootstrap - Felsenstein - 1985
3665	Modeltest: testing the model of DNA substitution. - Posada, KA - 1998
1943	MRBAYES: Bayesian inference of phylogenetic trees - JP, Ronquist
1884	Evolutionary trees from DNA sequences: A maximum likelihood approach - Felsenstein - 1981
1457	PAML: a program package for phylogenetic analysis by maximum likelihood. - Yang - 1997
621	Cases in which parsimony or compatibility methods will be positively misleading - Felsenstein - 1978
376	Comparison of phylogenetic trees - Robinson, Foulds - 1981
287	A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. - Lartillot, Philippe - 2004
279	Bayesian Phylogenetic Inference using DNA Sequences: A Markov Chain Monte Carlo Method - Yang, Rannala - 1997
276	Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. - Yang - 1993
203	Bayesian phylogenetic analysis of combined data. - JAA, Ronquist, et al. - 2004
192	Combining data in phylogenetic analysis. - Huelsenbeck, Bull, et al. - 1996
173	Phylogeny estimation and hypothesis testing using maximum likelihood. - Huelsenbeck, Crandall - 1997
135	A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. - Pagel, Meade - 2004
133	Selecting the best-fit model of nucleotide substitution. - POSADA, CRANDALL - 2001
132	Maximum likelihood models for combined analyses of multiple sequence data. - Yang - 1996
130	Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. - MOORE - 1995
112	Gene trees and species trees: molecular systematics as one-character taxonomy. - Doyle - 1992
103	Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. - KOLACZKOWSKI, THORNTON - 2004
102	JD: Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature - Bergthorsson, KL, et al. - 2003
97	Parsimony jackknifing outperforms neighbor-joining. - Farris, Albert, et al. - 1996
90	Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. - Felsenstein - 1973
82	Performance of phylogenetic methods in simulation. - HUELSENBECK - 1995
79	Arthropod phylogeny based on eight molecular loci and morphology. Nature, 413:157–161. Effi cient tree searches with available algorithms Evolutionary Bioinformatics 2007:3 - Giribet, Edgecombe, et al. - 2006
78	Modeling the covarion hypothesis of nucleotide substitution. - Tuffley, Steel - 1998
71	Maximum-likelihood phylogenetic analysis under a covarion-like model. - Galtier - 2001
68	Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. - Suzuki, Glazko, et al. - 2002
63	Should we use model-based methods for phylogenetic inference when we know assumptions about among-site rate variation and nucleotide substitution pattern are violated? - Sullivan, SwoVord - 2001
61	Comparing bootstrap and posterior probability values in the four-taxon case. - Cummings, Handley, et al. - 2003
60	Sampling properties of DNA sequence data in phylogenetic analysis. - CUMMINGS, OTTO, et al. - 1995
59	Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates. Systematic Biology - Graybeal - 1994
54	Success of maximum likelihood phylogeny inference in the four-taxon case. - GAUT, F - 1995
54	Molecular versus morphological approaches to systematics. - Hillis - 1987
50	The importance of proper model assumption in Bayesian phylogenetics. - Lemmon, Moriarty - 2004
50	Phylogenetic analysis using parsimony and likelihood methods. - Yang - 1996
48	Heterotachy, an important process of protein evolution. - Lopez, Casane, et al. - 2002
43	An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution - WM, Markowitz - 1970
40	Best-fit maximum likelihood models for phylogenetic inference: empirical tests with known phylogenies. - Cunningham, Zhu, et al. - 1998
40	Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. - Jow, Hudelot, et al. - 2002
39	Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. - FE, DL - 2004
39	The use of tree comparison metrics. - Penny, HendyMD - 1985
37	Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. - CHANG - 1996
36	Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). - Baker, Wilkinson, et al. - 2001
33	Arthropod phylogeny: a combined approach. - WHEELER, CARTWRIGHT, et al. - 1993
27	Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. - Graham, Olmstead - 2000
26	Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol - Gadagkar, Kumar - 2005
26	A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Molecular Biology and Evolution 15:1183–1188. - Lockhart, Steel, et al. - 1998
25	The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support - Buckley, Cunningham - 2002
25	A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae - Caterino, Reed, et al. - 2001
25	An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data - Taylor, Piel - 2004
24	Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome Inform - Waddell, Kishino, et al. - 2002
23	Holzenthal R: Phylogeny of Trichoptera (caddisflies): Characterization of signal and noise within multiple datasets. Syst Biol 2001 - Kjer, Blahnik
23	S: Horizontal gene transfer from flowering plants to Gnetum - Won, Renner
22	Interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus - Reed, Sperling - 1999
19	A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. - EA, MM - 2005
18	Group II introns as phylogenetic tools: structure, function and evolutionary constraints - Kelchner - 2002
14	Parametric phylogenetics? - SANDERSON, KIM - 2000
14	Support for a monophyletic lemuriformes: overcoming incongruence between data partitions. - Stanger-Hall, Cunningham - 1998
13	Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny - Barkman, Chenery, et al. - 2000
9	Prior agreement: arbitration or arbitrary? Syst - Siddall - 1997
9	Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. - Simmons, Miya - 2004
8	Maximum likelihood analysis of gene-based and structure-based process partitions, usingmammalianmitochondrial genomes. Syst. Biol - DEBRY - 1999
8	Hydrophobicity and phylogeny. - NAYLOR, COLLINS, et al. - 1995
7	Hybridization, introgression, and linkage evolution. - Rieseberg, Baird, et al. - 2000
6	Molecular and morphological data provide phylogenetic resolution at different hierarchical levels in Andira. - Pennington - 1996
5	Character-state space versus rate of evolution in phylogenetic inference,” - Simmons, Reeves, et al. - 2004
4	Inference of higher-order relationships in the cycads from a large chloroplast data set. - Rai, O’Brien, et al. - 2003
2	Phylogeny of the Celastraceae, inferred from 26S nuclear ribosomal DNA, phytochrome - Simmons, Savolainen, et al. - 2001
1	Empirical problems of the hierarchial likelihood ratio test for model selection - Pol - 2004
1	et al. / Cladistics 22 (2006) 171–185 - Simmons - 1998
1	How meaningful are Bayesian posterior probabilities - Simmons, Pickett, et al.