ライフサイエンスコーパス: parsimony

1 ation data sets, respectively; P = .048) and parsimony.

2 itive, site-pattern-oriented approaches like parsimony.

3 unctional impact predictor that is guided by parsimony.

4 n must therefore be excercised in the use of parsimony.

5 ees are obtained by the criterion of maximum parsimony.

6 it improves predictions without sacrificing parsimony.

7 character state cannot change to itself with parsimony.

8 hed that these compounds are used with great parsimony.

9 angements and phylogeny can be unified under parsimony.

10 roximal femur evolution using squared-change parsimony.

11 the direction of the TE-gene relationship by parsimony.

12 We also devised a new maximum parsimony algorithm that, given the states of the sample

13 yzed using Bayesian, maximum likelihood, and parsimony algorithms to determine whether the individual

14 m likelihood, minimum evolution, and maximum parsimony analyses all contradict macroglossine monophyl

15 Maximum-likelihood, neighbor-joining, and parsimony analyses also suggested as less likely E. hist

16 Parsimony analyses of amino acid sequences and maximum l

17 Parsimony analyses of combined and partitioned data sets

18 Here we report the results of parsimony analyses of DNA sequences of the plastid genes

19 molecular phylogenies are incorporated into parsimony analyses of morphological characters, includin

20 ported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA s

21 Parsimony analyses unambiguously indicate that the four

22 m-likelihood, minimum-evolution, and maximum-parsimony analyses yielded congruent phylogenies support

23 As an alternative to parsimony analyses, stochastic models have been proposed

24 Parsimony analysis and coalescent theory suggest that th

25 basal relationships established with maximum parsimony analysis except two are present in the distanc

26 ,000 bp per taxon) for 16 taxa, (ii) maximum parsimony analysis for a subset of these genes for 104 t

27 e craniodental characters were adjusted in a parsimony analysis for the primate tribe Papionini, a gr

28 Maximum parsimony analysis is used to separate the evolution of

29 Parsimony analysis of CGG repeat substructure within thi

30 Amino acid alignments and a parsimony analysis of nucleotide alignments show the ska

31 Results were compared to a parsimony analysis of spore morphological characters of

32 We performed maximum-parsimony analysis of the 359 sequences and calculated t

33 Parsimony analysis of the aligned 18S and 28S DNA sequen

34 Parsimony analysis of the combined data set comprising 7

35 Parsimony analysis of the FMR1 CGG repeat substructure p

36 simulated evolution) and those inferred from parsimony analysis of the resulting character data, with

37 Parsimony analysis of the SVR sequences yielded a dendro

38 Parsimony analysis placed the Rhinosporidium ITS sequenc

39 However, in older African populations, parsimony analysis predicts the occasional loss of an AG

40 Parsimony analysis reveals two main clades and suggests

41 Phylogenies based on distances and parsimony analysis show that all plant catalases derive

42 Maximum parsimony analysis suggests that an ancestral L71 gene d

43 Parsimony analysis suggests that this fossil represents

44 networks obtained by Templeton's statistical parsimony analysis were generated for combined (concaten

45 Parsimony analysis yielded a subgroup including the B. c

46 nd a clustering method based on phylogenetic parsimony analysis), we assessed the lineage relationshi

47 ted in the levels of homoplasy detected in a parsimony analysis, because higher numbers of states per

48 history of the laboratory mouse using Wagner parsimony analysis.

49 results and those inferred by commonly-used parsimony and Bayesian methods demonstrates that statist

50 present phylogenetic analyses using maximum parsimony and Bayesian methods that address the origin a

51 data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well sup

52 Parsimony and Bayesian phylogenetic analyses showed that

53 The parsimony and Bayesian results are highly congruent, and

54 ical complications, as the best solution for parsimony and clinical meaningfulness.

55 Both parsimony and cluster analyses were used to divide the g

56 intergenic spacer was analyzed using maximum parsimony and compared with nuclear ITS rDNA using a sim

57 Parsimony and distance analyses further identify purple

58 Parsimony and distance analysis of the separate genes we

59 Maximum-parsimony and distance methods revealed distinct SV40 cl

60 Using phylogenetic analysis, by parsimony and distance methods, of R. seeberi's 18S SSU

61 A useful risk-adjustment model must balance parsimony and ease of data collection with predictive ab

62 Parsimony and energetics would suggest a one-step mechan

63 Maximum parsimony and isolation-by-distance analyses revealed li

64 tal duplications in the human genome in both parsimony and likelihood settings.

65 We introduce parsimony and likelihood techniques to analyze the evolu

66 adjacent markers, the method first combines parsimony and likelihood to build an evolutionary tree o

67 The methods we evaluated include parsimony and likelihood using the single best reconstru

68 Maximum parsimony and maximum likelihood analyses of 27 publicly

69 le sequence alignment using distance matrix, parsimony and maximum likelihood approaches to infer the

70 We have developed weighted parsimony and maximum likelihood methods for inferring g

71 Parsimony and maximum likelihood methods of phylogenetic

72 d and contrasted with the results of maximum parsimony and maximum likelihood methods.

73 re tool to infer gene family histories using parsimony and maximum likelihood.

74 Maximum-parsimony and maximum-likelihood analyses of aligned DNA

75 logies and estimating these parameters using parsimony and maximum-likelihood methods for each of the

76 ondary structural features, and subjected to parsimony and neighbor joining distance analysis.

77 rees were constructed using both the maximum parsimony and neighbor joining methods of the PHYLIP(3.5

78 e.g., 100% bootstrap value with both maximum parsimony and neighbor joining).

79 a single outgroup species and were based on parsimony and neighbor joining.

80 Phylogenetic analysis using parsimony and neighbor-joining algorithms identified fiv

81 upported by high bootstrap values in maximum-parsimony and neighbor-joining analyses and were confirm

82 This result, based on parsimony and neighbor-joining analyses of primary amino

83 d human ABC genes were examined with maximum parsimony and neighbor-joining analyses that demonstrate

84 Protein parsimony and protein distance matrix analyses show that

85 In seeking a compromise between parsimony and realism, we introduce a class of metapopul

86 deep coalescence, matrix representation with parsimony and the greedy consensus.

87 We analyze it with parsimony and, for the first time for a tyrannosauroid d

88 y application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data se

89 Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genet

90 Maximum likelihood, maximum parsimony, and Bayesian methods were used to infer phylo

91 xamined for their percent of total variance, parsimony, and clinical interpretability.

92 ce matrix, using maximum likelihood, maximum parsimony, and compatibility methods.

93 F(ST) calculations, parsimony, and distance analysis demonstrated relationsh

94 and fungi, using maximum likelihood, maximum parsimony, and distance methods.

95 of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phyl

96 red mutations causing births/deaths based on parsimony, and investigated local genomic environments a

97 for phylogenetic information using distance, parsimony, and likelihood approaches.

98 ic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA g

99 nes using a combination of distance, maximum parsimony, and maximum likelihood methods indicate that

100 neighbor-joining, minimum evolution, maximum parsimony, and maximum likelihood methods.

101 ne analyses using minimum evolution, maximum parsimony, and maximum likelihood phylogenetic methods,

102 minimum evolution-neighbor joining, maximum parsimony, and maximum likelihood, we address overall le

103 sequences performed using distance, maximum-parsimony, and maximum-likelihood approaches yielded con

104 reconstructions with distance-based, maximum-parsimony, and maximum-likelihood methods.

105 Maximum likelihood, parsimony, and neighbor joining methods all supported a

106 imum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree r

107 re we implemented distance matrices, maximum parsimony, and neighbor-joining analyses to assess the e

108 Parsimony- and codon model-based phylogenetic analysis o

109 Parsimony- and likelihood-based analyses of plastid rbcL

110 Both parsimony- and likelihood-based estimates of the gamma-d

111 Using an empirical parsimony approach (AdaptML) we have investigated the di

112 Using a parsimony approach ancestral structural states could be

113 While a gene tree parsimony approach can be informative about genome evolu

114 By employing a maximum parsimony approach to compare repertoires of Pfam domain

115 ollections of gene trees using the gene tree parsimony approach.

116 Here we show that maximum parsimony approaches previously used to reconstruct evol

117 Gene tree parsimony approaches seek the evolutionary scenario that

118 If ancestral sequences predicted by parsimony are to be regarded as actual historical sequen

119 I present here a simple parsimony-based analysis that suggests that East Asians

120 In conclusion, ParsSNP uses an innovative, parsimony-based approach to prioritize cancer driver mut

121 e in the observed network data than a simple parsimony-based approach.

122 cy with metabolic gene functions compared to parsimony-based approaches.

123 The algorithm further uses Dollo parsimony-based comparison of the inferred ancestral gen

124 The parsimony-based estimate of Ts/Tv from the well-corrobor

125 mum-likelihood estimation is three times the parsimony-based estimate, suggesting that parsimony-base

126 he parsimony-based estimate, suggesting that parsimony-based estimates are severe underestimates even

127 RNA metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant gr

128 ed more biologically relevant solutions than parsimony-based gap filling approaches.

129 s (a distance-based LWL85 model) and SNAP (a parsimony-based NG86 model) made pairwise comparisons of

130 Parsimony-based optimization of character states on our

131 We develop a parsimony-based phylogenetic method for protein sequence

132 Distance- and parsimony-based phylogenetic trees are consistent and re

133 derm organogenesis demonstrated that maximum parsimony-based reconstruction of developmental trees re

134 Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks.

135 Parsimony-based relative rate tests for amino acid chang

136 Phylogenetic analyses (parsimony, Bayesian, maximum likelihood) showed the clea

137 estral reconstruction, we recommend weighted parsimony because it has similar accuracy to maximum lik

138 om the whole-brain networks that may suggest parsimony between multiple accounts of cognitive control

139 Maximum parsimony can be considered nonparametric, because trees

140 The analysis demonstrates that parsimony can be misleading even when levels of sequence

141 The trees generated by parsimony confirmed the monophyletic taxonomic placement

142 ry advantage over current instruments is its parsimony, containing only 6 items.

143 f networks, "softwired" and "hardwired." The parsimony cost of hardwired networks is based on all cha

144 red, where each character follows the lowest parsimony cost tree displayed by the network, resulting

145 of the i.i.d. model to observed and expected parsimony counts, that is, from constant sites, to singl

146 nformation: hierarchical groups emerge via a parsimony criterion in nested cladistic analysis but mus

147 riation significantly outperform the maximum parsimony criterion in phenotypic accuracy.

148 e with a nonbinary species tree under a DTLI parsimony criterion.

149 itness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network recons

150 common methods of phylogeny reconstruction--parsimony, distance and maximum likelihood--differ in th

151 as true for phylogenetic reconstruction with parsimony, distance, and likelihood methods.

152 Parsimony, distance, and maximum-likelihood analyses of

153 methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods.

154 Alternative methods - such as maximum parsimony - explicitly take the tree structure into acco

155 Maximum parsimony favored a lungfish/coelacanth or a lungfish/te

156 The preferred model (based on fit and parsimony) for predicting the odds of one or more deaths

157 ets and then reconciling the two trees under parsimony framework.

158 redict the states for Se-related traits in a parsimony framework.

159 We developed a method for maximum-parsimony haplotype frequency estimation from pooled DNA

160 By contrast, maximum parsimony has been shown to be accurate only when this r

161 ee, and that maximum likelihood and weighted parsimony have similar accuracy for reconstructing the a

162 oach (EMBP: Entropy Minimization and Boolean Parsimony) identifies sets of synergistically interactin

163 points) with the requirement of statistical parsimony (ie, the need to reduce the number of interpre

164 al how nature, despite being popular for its parsimony in recycling functional motifs, can use differ

165 of constant frequency afford us significant parsimony in the generation and testing of candidate ove

166 liation is typically performed using maximum parsimony, in which each evolutionary event type is assi

167 ls of sequence divergence are as low as 10%; parsimony incorrectly infers an excess of common to rare

168 m 16S rRNA gene sequences using distance and parsimony indicated that the CLB from proliferative gill

169 t is, from constant sites, to singletons, to parsimony informative characters of a minimum possible l

170 first inferring a full distribution of both parsimony-informative and non-informative pattern joint

171 om noncoding regions increased the number of parsimony-informative characters and lengthened short in

172 ascertainment bias, in that only varying, or parsimony-informative characters are observed.

173 rmative pattern joint probabilities from the parsimony-informative ones, using phylogenetic invariant

174 However, it is known that parsimony is biased when the base composition of the DNA

175 Parsimony is commonly used to infer the direction of sub

176 um structural diversity from maximal genetic parsimony is conferred by a simple translational switch

177 tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the

178 Maximum parsimony is one of the most commonly used criteria for

179 aches perform well most of the time, maximum parsimony is strongly biased towards recovering an incor

180 Parsimony, likelihood, and distance methods can all be u

181 hanisms; and (ii) in a remarkable example of parsimony, loop L2 is a molecular switch that controls b

182 Maximum parsimony, maximum likelihood, and Bayesian analyses of

183 We report here (i) maximum parsimony, maximum likelihood, and Bayesian phylogenetic

184 Parsimony, maximum likelihood, and distance methods were

185 Data were analyzed using maximum parsimony, maximum likelihood, and neighbor joining.

186 e-evolution simulation program that compares parsimony, maximum likelihood, and the Bayesian methods

187 an inconsistency in the criterion of maximum parsimony-maximum parsimony trees for different groups o

188 Sequences were clustered by use of a parsimony method and the virological responses (ratio of

189 The performance of both variants of the parsimony method are competitive to the performance of t

190 The parsimony method has a very low rate of false positives

191 The parsimony method of Suzuki and Gojobori and the maximum

192 phylogenetic tree as inferred by the maximum parsimony method.

193 hylogenetic analyses which generally use the parsimony method.

194 a variant lineage determined by phylogenetic parsimony methods based on URR/E6 sequences.

195 Evolutionary analysis using parsimony methods confirmed the differences between the

196 methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central

197 joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic t

198 analysis with maximum likelihood and maximum parsimony methods showed the sequence to be most closely

199 congruent dendrograms based on distance and parsimony methods suggested that the restriction fragmen

200 ) were analysed using maximum likelihood and parsimony methods to estimate asymmetries in rates of ch

201 top algorithms for this problem even though parsimony methods use less information than some of the

202 ce-based methods (such as neighbor-joining), parsimony methods using sequence-based encodings, Bayesi

203 -likelihood, Bayesian-inference, and maximum-parsimony methods.

204 For example, parsimony minimizes the number of mutations, which biase

205 results quantify the limitations of the Pure Parsimony model and demonstrate the imperative need to c

206 can isolates and 12 U.S. isolates by maximum-parsimony (MP) and maximum-likelihood (ML) analyses, wit

207 In the maximum parsimony (MP) and minimum evolution (ME) methods of phy

208 In the maximum parsimony (MP) method, the tree requiring the minimum nu

209 alysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms s

210 e Bayesian, maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) methods with d

211 by two currently available methods (maximum-parsimony [MP] and maximum-likelihood [ML] methods) in a

212 also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using

213 sliding-window similarity measures; maximum-parsimony, neighbor-joining, and Bayesian phylogenetic a

214 Phylogenetic analyses employing maximum parsimony, neighbor-joining, and maximum likelihood meth

215 All phylogenetic analyses (maximum parsimony, neighbor-joining, and maximum likelihood) poi

216 Phylogenetic trees constructed using maximum parsimony, neighbor-joining, Fitch-Margolish, or maximum

217 not observed for a key one-step clade in the parsimony network.

218 Parsimony networks constructed of haplotypes from both s

219 tudy demonstrates the utility of statistical parsimony networks for the detection of hybrids in the g

220 rticular, we show that our novel and robust 'parsimony' normalization method is superior to the widel

221 ork we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provi

222 ween malaria diagnostics and the utility and parsimony of employing a sample pooling strategy for mol

223 This article examines the parsimony of haplotypes using known haplotypes as well a

224 the basis of both data-fitting criteria and parsimony of the regulatory processes, ruling out biolog

225 In part, this is the parsimony of viruses, where a minimal number of proteins

226 cies in J, for example by the use of maximum parsimony on those four species alone.

227 hylogenetic networks to compete equally on a parsimony optimality basis.

228 uracy of the more elaborate methods based on parsimony or likelihood at a fraction of the computation

229 stematic biases resulted from (i) the use of parsimony or likelihood with SBR, (ii) the use of a stat

230 ived and ancestral states can be assigned by parsimony or on the basis of relative probability.

231 haracters at the tips using the criterion of parsimony over a set of bootstrap trees.

232 Maximum parsimony performs substantially better than current par

233 Maximum parsimony phylogenetic analyses, as well as Neighbor-Joi

234 are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing m

235 used in both maximum likelihood and maximum parsimony phylogenetic analyses.

236 ed Bayesian, maximum likelihood, and maximum parsimony phylogenetic analyses.

237 rearrangement algorithm to improve gene tree parsimony phylogenetic analyses.

238 um likelihood, neighbor joining, and maximum parsimony phylogenetic comparisons show that the alpha-a

239 Analysis by maximum-parsimony phylogenetic methods revealed 25 nucleotide di

240 Maximum parsimony phylogenetic tree reconciliation is an importa

241 topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylog

242 form large-scale inferences of local maximum parsimony phylogenies from single nucleotide polymorphis

243 nomic scale, we develop a library of maximum parsimony phylogenies within local regions spanning all

244 These pathways are ranked using a parsimony principle, whereby scenarios requiring the few

245 This is equivalent to the Maximum Parsimony problem when the input sequences are not align

246 history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconst

247 ave models with good prediction accuracy and parsimony property.

248 trohelids as sisters to haptophytes, whereas parsimony puts them as sisters to red algae, but there i

249 In a tree that emphasizes cleavage parsimony, radial cleavage, regulative development, and

250 begins with a potentially infeasible maximum parsimony reconciliation and iteratively "repairs" it un

251 Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that hos

252 oblem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current method

253 whereas filtered total mercury did not meet parsimony requirements.

254 not incompatible with, evolved design, while parsimony requires explanatory adequacy and predictive a

255 ne haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be iden

256 lasses is robust with respect to alternative parsimony rules for inferring the presence of precursor

257 s strong statistical support in favor of the parsimony scenarios of 10 major chromosomal rearrangemen

258 to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phyloge

259 A similar strategy could be adopted with parsimony scores.

260 This fact suggests that parsimony should be enforced in estimation of haplotype

261 In the last two cases the parsimony solutions have very small probability.

262 were performed using both distance-based and parsimony strategies.

263 l shape characters may explain why published parsimony studies have diverged and filling three major

264 Parsimony suggests that increased growth and convolution

265 nzees' capacity for culture, a richness that parsimony suggests was shared with our common ancestor.

266 "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-f

267 e trees, but with other distance methods and parsimony the sole amoebozoan species branches weakly wi

268 In the interest of parsimony, the present work employed parametric sensitiv

269 del complexity according to the Principle of Parsimony to prefer simpler models as the signal-to-nois

270 unconstrained DNA sequences, we used maximum parsimony to separate phylogenetic trees of a non-long t

271 compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, thou

272 netic analyses have turned away from maximum parsimony towards the probabilistic techniques of maximu

273 escribe major changes in the topology of the parsimony tree and provide names for new and rearranged

274 A parsimony tree for the M. musculus mtDNAs is about half

275 e species in S, then U need not be a maximum parsimony tree for the species in K.

276 Unfortunately, when T is a maximum parsimony tree for the species in S, then U need not be

277 The rooted parsimony tree of Rps2 sequences drawn from a diverse se

278 e Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplo

279 mon method selects for such a tree a maximum parsimony tree using the genome of the species in S.

280 vailable, but the methods for likelihood and parsimony trees are yet to be refined.

281 n the criterion of maximum parsimony-maximum parsimony trees for different groups of species may be "

282 synonymous SNPs was compared to the maximum parsimony trees inferred from pulsed-field gel electroph

283 The parsimony trees showed no branches correlating with the

284 construct phylogenetic trees via the maximum parsimony, Unweighted Pair Group Method with Arithmetic

285 This is a known problem with parsimony using outgroup species.

286 Models were evaluated for parsimony, using Akaike's Information Criterion.

287 t likely number of events is larger than the parsimony value.

288 cal aspects of genomic trees-e.g., comparing parsimony versus distance-based approaches and examining

289 Phylogenetic reconstructions by parsimony were carried out on an enlarged body of primat

290 inferring phylogenies make this assumption; parsimony, when valid, is less limited by it.

291 type configurations was constructed by using parsimony with a single-step mutation model.

292 rthropods to evolve an elegant semiochemical parsimony with which to exploit the biological milieu.