ライフサイエンスコーパス: phylogenetic tree

1 t isolates used to determine the root of the phylogenetic tree).

2 cell shape appears throughout the bacterial phylogenetic tree.

3 GenBank, we constructed a maximum-likelihood phylogenetic tree.

4 e been made to internal nodes of a reference phylogenetic tree.

5 patients were more widely distributed in the phylogenetic tree.

6 s only when inconsistent with most taxa in a phylogenetic tree.

7 torial constraints defined by the underlying phylogenetic tree.

8 re members of subfamily I of the bromodomain phylogenetic tree.

9 n the birth and death rates of lineages in a phylogenetic tree.

10 volutionary process that can be modeled as a phylogenetic tree.

11 rior distribution is designed to utilize the phylogenetic tree.

12 ral different approaches being used to infer phylogenetic tree.

13 e corresponding transmission clusters from a phylogenetic tree.

14 tribution of consciousness across the animal phylogenetic tree.

15 anges along the path connecting viruses in a phylogenetic tree.

16 rstand eye development in animals across the phylogenetic tree.

17 aced within UGT clades of the C. trachomatis phylogenetic tree.

18 expansion or loss occurred on the angiosperm phylogenetic tree.

19 according to their relationships in plants' phylogenetic tree.

20 preferentially located on the "trunk" of the phylogenetic tree.

21 place or source of isolation, mapped on the phylogenetic tree.

22 geographic movements along the branches of a phylogenetic tree.

23 he pulvinar is consistent across the primate phylogenetic tree.

24 d in metagenomic research, but it requires a phylogenetic tree.

25 mily, while simultaneously inferring a dated phylogenetic tree.

26 on to incorporate annotations throughout the phylogenetic tree.

27 demics, and constructed a maximum likelihood phylogenetic tree.

28 ing in unsequenced branches of the microbial phylogenetic tree.

29 d trait patterns observed at the tips of the phylogenetic tree.

30 sion in sensitivity to herbicides within the phylogenetic tree.

31 ure in microbial community data encoded by a phylogenetic tree.

32 te parameters of gene gain and loss across a phylogenetic tree.

33 F specificity that can be applied across the phylogenetic tree.

34 with a newly generated time-calibrated mega-phylogenetic tree.

35 al in the data without requiring an explicit phylogenetic tree.

36 cks quality, suggests a taxonomy and draws a phylogenetic tree.

37 of sequence similarity measures to construct phylogenetic trees.

38 e DNA regions to reconstruct high-confidence phylogenetic trees.

39 approaches from ancestor-descendant pairs to phylogenetic trees.

40 the interpretation of the relationship among phylogenetic trees.

41 relationship among a large set of competing phylogenetic trees.

42 lysed using multiple sequence alignments and phylogenetic trees.

43 ikelihood and Bayesian analyses yield robust phylogenetic trees.

44 o all currently sequenced strains of VARV on phylogenetic trees.

45 elationships within OGs based on analysis of phylogenetic trees.

46 ods are well suited for constructing massive phylogenetic trees.

47 eduction and visualization over the space of phylogenetic trees.

48 al projective space rather than the space of phylogenetic trees.

49 e large sets of gene trees over the space of phylogenetic trees.

50 akes SNP data directly as input and produces phylogenetic trees.

51 nt prevalence thresholds and across multiple phylogenetic trees.

52 or experimental design and reconstruction of phylogenetic trees.

53 t-curated annotations of protein families on phylogenetic trees.

54 ists to quantify similarity between pairs of phylogenetic trees.

55 roviding a means to "break" long branches in phylogenetic trees.

56 ons of GO terms based on annotated reference phylogenetic trees.

57 atively impacts the accuracy of the inferred phylogenetic trees.

58 in a reference data set, or for constructing phylogenetic trees.

59 tating protein sequences using pre-annotated phylogenetic trees.

60 show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the

61 Phylogenetic tree also showed close relationship of RbTI

62 Structural alignment and phylogenetic tree analysis indicate that StnA represents

63 r 18 out of 34 MS patients when evaluated by phylogenetic tree analysis.

64 equenced strains from Pakistan in a combined phylogenetic tree analysis.

65 ssumptions, such as a shared topology of the phylogenetic tree and a lack of within-host diversity.

66 analysis of enzymes dispersed within the PL2 phylogenetic tree and elucidated the structure of VvPL2

67 Simulations are guided by a phylogenetic tree and incorporate different substitution

68 nome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of s

69 eb-based tool to interactively visualize the phylogenetic tree and spatial distribution of clones in

70 alization of type IV isolates in a SNP-based phylogenetic tree and suggested that ST-452 could have o

71 y of rheumatic fever-associated strains in a phylogenetic tree and to identify the presence of 10 pre

72 s is very heterogeneously distributed on the phylogenetic tree and varies little with range size or t

73 Neighbour-joining phylogenetic trees and direct sequence comparison were u

74 Here we analyze a large collection of phylogenetic trees and fossil time series and describe a

75 Both phylogenetic trees and networks are typically reconstruc

76 Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate anal

77 The results of genetic distances, phylogenetic trees and principal component analysis reve

78 uce contact networks, transmission networks, phylogenetic trees and sequence datasets, and to add err

79 st adjustment (penalty) is proposed to allow phylogenetic trees and soft-wired phylogenetic networks

80 and users can select from a range of stored phylogenetic trees and spatial datasets, or upload their

81 We inferred maximum-likelihood phylogenetic trees and time trees containing a fragment

82 the evolution of phenotypic traits, based on phylogenetic trees and trait measurements of extant spec

83 Efforts to reconstruct phylogenetic trees and understand evolutionary processes

84 -temporal information contained in estimated phylogenetic trees and uses this information to calculat

85 l's tau-distance, which does not depend on a phylogenetic tree, and hence more readily applicable to

86 al BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spect

87 equences of ancestral proteins at nodes in a phylogenetic tree, and the history of each amino acid ca

88 s must import the microbiome data, integrate phylogenetic trees, and access and merge public and rest

89 ed for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic

90 e DRC and other countries were visualized in phylogenetic trees, and isolates representing distinct l

91 Our approach differs from traditional phylogenetic tree approaches in that our mutation tree d

92 control, methods that take into account the phylogenetic tree are largely limited.

93 Phylogenetic trees are essential for studying biology, b

94 rd putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary

95 abundance data, public patient metadata, and phylogenetic trees as a single data object.

96 us time Markov Chain along the branches of a phylogenetic tree attached with five extended branches l

97 e of the EF-1a gene was higher than COI, and phylogenetic tree based on EF-1a showed that haplotypes

98 alled StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along w

99 The phylogenetic tree based on the receptor-determining regi

100 Phylogenetic trees based on different data sets were con

101 We built phylogenetic trees based on genomic sequences of functio

102 clusters were identified by construction of phylogenetic trees based on HCV NS5B (genotype 1a/4d) or

103 P2CS also provides phylogenetic trees based on the conserved signaling doma

104 ing maximum-likelihood and Bayesian methods, phylogenetic trees based on the full-length S, M and L s

105 Phylogenetic trees based on these two analyses were very

106 We have included a phylogenetic tree, based on 16S rRNA sequences, which co

107 can play an important complementary role to phylogenetic tree-based analysis, such as is done in the

108 signatures: genetic diversity, variation in phylogenetic tree branch lengths, and tree height.

109 g and spectral karyotyping-based single-cell phylogenetic tree building, we show two distinct types o

110 retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct te

111 ent of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction.

112 in which the authors reconstructed subclonal phylogenetic trees by manual expert curation, we show ho

113 ly extends the alignment and infers extended phylogenetic trees by using previously inferred smaller

114 Based on a molecular phylogenetic tree calibrated using fossils, including th

115 cture of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to K

116 Using our framework, large phylogenetic trees can be perpetually updated without hu

117 ple, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs

118 lifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and Eur

119 ltaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency w

120 h quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available

121 A phylogenetic tree consisting of GH26 enzymes revealed fo

122 Accordingly, a phylogenetic tree constructed with sequences derived fro

123 Gram-negative bacteria were calculated, and phylogenetic trees constructed.

124 This package aims to improve the quality of phylogenetic tree construction especially in instances o

125 erpret hypothesis test results, which inform phylogenetic tree construction, and we introduce the fir

126 and function prediction, gene annotation and phylogenetic tree construction.

127 A phylogenetic tree could also be constructed directly fro

128 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models.

129 es and the differences can be used to create phylogenetic trees depicting relatedness among the sampl

130 Genomic tools, including phylogenetic trees derived from sequence data, are incre

131 Phylogenetic trees describe both the evolutionary proces

132 ures: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of

133 r the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its ma

134 Dating of phylogenetic trees estimated that these clones diverged

135 Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for g

136 ts are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal g

137 In addition, the backbones of phylogenetic trees exhibit bursts of diversification on

138 ith their worm-like bodies and behavior (see phylogenetic tree; Figure 1); Bivalvia (mussels and clam

139 en a challenging task to build a genome-wide phylogenetic tree for a large group of species containin

140 ining species to analyze, and the associated phylogenetic tree for all organisms involved.

141 We built a phylogenetic tree for Cyprinodontiformes, an order in wh

142 wed by clonal deconvolution to reconstruct a phylogenetic tree for each tumor.

143 We constructed phylogenetic trees for 794 subtype A1 and 64 subtype B s

144 ielded highly supported and nearly identical phylogenetic trees for all major avian lineages.

145 econstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresp

146 By building phylogenetic trees for key enzymes in 24-ipc biosynthesi

147 ions, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago trun

148 Yet inferring reliable phylogenetic trees for thousands of species involves num

149 e of the earliest methods for constructing a phylogenetic tree from a distance matrix, remains open.

150 ferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is

151 We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in C

152 Comparisons of the phylogenetic trees from brain tissues revealed that DNA-

153 um likelihood is building maximum likelihood phylogenetic trees from protein alignments.

154 Steroid hormones are produced throughout the phylogenetic tree, from plants to mammals.

155 The phylogenetic tree, gene structures and conserved motifs

156 In the SSU phylogenetic tree generated in the present study, Synste

157 Analyses of phylogenetic trees generated by cgMLST displayed a high

158 In phylogenetic trees, GlyT2-like sequences from invertebra

159 We inferred their phylogenetic trees in 69 sequenced chordate genomes.

160 Although the use of phylogenetic trees in epidemiological investigations has

161 over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 10

162 receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GP

163 Sequence alignment and phylogenetic tree indicated that some serpins similar to

164 community-onset and HO-USA300 strains on the phylogenetic tree indicates that these strains derive fr

165 occurred in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection i

166 n occurs in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection i

167 ched on the trunk versus the branches of the phylogenetic tree, indicating that viruses that acquire

168 apitulated the topological structures of the phylogenetic trees, indicating a possible relationship b

169 PASTRI provides a robust approach for phylogenetic tree inference from mixed samples.

170 The impact of both dimensions of scale on phylogenetic tree inference has been well characterized

171 tandalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of

172 We find that, as in the case of phylogenetic tree inference, the performance of leading

173 TreeFam is a database of phylogenetic trees inferred from animal genomes.

174 Phylogenetic trees inferred from core-genome single nucl

175 Phylogenetic trees inferred from mitochondrial genes ret

176 Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of inde

177 Thus, incorporating the phylogenetic tree information can potentially improve th

178 rther extend our method by incorporating the phylogenetic tree into the normalization process.

179 el marginal likelihood, allowing us to split phylogenetic trees into clades and subclades using a pop

180 . host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach.

181 When the phylogenetic tree is mis-specified or non-informative, o

182 The distribution of a phenotype on a phylogenetic tree is often a quantity of interest.

183 tially have an effect on whether the correct phylogenetic tree is recovered.

184 The estimation of phylogenetic trees is a major part of many biological da

185 However, the space of phylogenetic trees is not Euclidean, so ordinary machine

186 Close proximity of promoter sequences in phylogenetic trees is roughly reflected by similarity of

187 lest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new spe

188 diated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait

189 ce taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy.

190 mutation rates and their timing to determine phylogenetic tree morphologies.

191 lationships between genes are represented in phylogenetic trees, multiple sequence alignments and sta

192 pical principal components over the space of phylogenetic trees, namely, the existence of a tropical

193 Phylolink connects phylogenetic tree nodes with species occurrence records,

194 Phylogenetic trees now include inference of horizontal t

195 Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a sup

196 bacterial strains distributed throughout the phylogenetic tree of cyanobacteria.

197 we identified HCV codons that vary deep in a phylogenetic tree of HCV sequences and showed that a pol

198 des users with an expanded and daily updated phylogenetic tree of life (sTOL).

199 Construction of a phylogenetic tree of protein sequences maps out the like

200 haracterized beta-OHAsp diastereomers to the phylogenetic tree of siderophore beta-hydroxylases, meth

201 en shown by its ability to build the correct phylogenetic tree of species based solely on the topolog

202 loroplast loci to estimate a time-calibrated phylogenetic tree of the genus Corylus.

203 well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc

204 orrelated with their genetic distance in the phylogenetic tree of the paramyxovirus family.

205 a genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia.

206 We constructed phylogenetic trees of 29 Populus taxa using 80 individua

207 iling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences o

208 Phylogenetic trees of emrE grouped YSLPVs with algae, su

209 GC B cells expressing germline transcripts, phylogenetic trees of GC BCRs from secondary lymphoid or

210 lely on retroduplication variation, we built phylogenetic trees of human populations; these represent

211 biological, structural and chemical data on phylogenetic trees of human protein families involved in

212 , rely upon multiple sequence alignments and phylogenetic trees of large datasets.

213 Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conser

214 Thus, phylogenetic trees of prokaryotes can be constructed bot

215 es of cells from mapped reads and constructs phylogenetic trees of related cells.

216 FFP-based phylogenetic trees of seven gastric Helicobacter species

217 Whole-exome sequencing was used to construct phylogenetic trees of the PMNs and the ensuing HSTM clon

218 Found throughout the phylogenetic tree, often in drug-like roles, their size,

219 We constructed a calibrated phylogenetic tree on the basis of binary single-nucleoti

220 We simulate pathogen phylogenetic trees on dynamic Erdos-Renyi random network

221 e results show how dynamical scaling laws of phylogenetic trees on long timescales can reflect the in

222 atrix which can be directly used to generate phylogenetic trees or creates a tree from a shrunk genom

223 Our dated phylogenetic tree places Macrauchenia as sister to Peris

224 oth trees, utilising a newly-designed set of phylogenetic tree proposals that also respect node parti

225 Phylogenetic trees provide important insights into mecha

226 The resulting phylogenetic trees provided evidence for rapid and retic

227 rmation and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can

228 ongruence of the B. tabaci-host and Portiera phylogenetic trees provides strong support for the hypot

229 Phylogenetic tree reconciliation is a widely used method

230 Maximum parsimony phylogenetic tree reconciliation is an important techniq

231 We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-t

232 Phylogenetic trees reconstructed from molecular sequence

233 greedy alignment-free distance estimator for phylogenetic tree reconstruction based on the concept of

234 rcing key concepts in sequence alignment and phylogenetic tree reconstruction.

235 ere, we implemented large-scale gene-species phylogenetic tree reconstructions and reconciliations to

236 Branching events in phylogenetic trees reflect bifurcating and/or multifurca

237 ally distinct subclones and reconstructs the phylogenetic tree relating the subclones.

238 r dynamics data, stochastic simulations, and phylogenetic trees, respectively.

239 All phylogenetic trees revealed that C. volvulus was polyphy

240 last eukaryotic common ancestor (LECA) using phylogenetic trees, sensitive profile-versus-profile hom

241 interrogate and visualise variation within a phylogenetic tree setting.

242 GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organizatio

243 The phylogenetic tree showed a strong temporal-spatial struc

244 The BioDetection phylogenetic tree showed that all isolates of this outbr

245 orrelation of viral loads in cherries of the phylogenetic tree, showing that both models of character

246 Long branches on the phylogenetic tree signaled prolonged gaps in AFP surveil

247 Phylogenetic trees simulated with the recently reported

248 t was associated with more unbalanced tumour phylogenetic trees, suggesting the need of denser sampli

249 r mutations located on the branches of tumor phylogenetic trees targeted oncogenes, including PIK3CA,

250 This web-application displays a phylogenetic tree that can be decorated with additional

251 n GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all diffe

252 s somatic mutations into clones and infers a phylogenetic tree that describes the evolutionary histor

253 to 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning C

254 ltiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relat

255 in taxon abundances, and the existence of a phylogenetic tree that relates all bacterial species.

256 que characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species

257 er which a pathogen spreads and the pathogen phylogenetic trees that are obtained presents an opportu

258 d matched metastases to build well-supported phylogenetic trees that illuminate individual patients'

259 However, the phylogenetic trees that they report differ significantly

260 In a phylogenetic tree, the three B4Hs were closest to conife

261 vestigated horizontally using the tip of the phylogenetic tree through comparative studies of extant

262 We constructed a phylogenetic tree to identify clusters of linked infecti

263 One challenge is to link phylogenetic trees to patterns of transmission.

264 We compare our phylogenetic trees to previous estimates of mammal-wide

265 logs in the same species and have correlated phylogenetic trees to the same extent, or higher than ot

266 s, involving pairwise comparisons of protein phylogenetic trees, to predict the protein-protein inter

267 A Bayesian phylogenetic tree, together with associated dating analy

268 construct comparable, or even more accurate, phylogenetic tree topologies than the kmacs heuristic al

269 sis of the dynamics shows that the resultant phylogenetic tree topology is scale-invariant due to a s

270 tribution of the virus corresponded with the phylogenetic tree topology, some virus exchange was obse

271 An accurate phylogenetic tree underpins our understanding of the maj

272 d to estimate tropical PCs over the space of phylogenetic trees using a Markov Chain Monte Carlo appr

273 tion of cases, and constructed time-resolved phylogenetic trees using genomes from Thailand and elsew

274 equence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony, Unweighted

275 y in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.

276 A phylogenetic tree was constructed with 19 604 Swiss sequ

277 sembled and annotated, and a high-resolution phylogenetic tree was constructed.

278 the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequen

279 etermined because the branching order in the phylogenetic tree was inconsistent with the order of iso

280 Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants h

281 To build a phylogenetic tree, we propose first representing each of

282 lutionary rate changes along the branches of phylogenetic trees, we show that the cerebellum underwen

283 The amino acid motifs and phylogenetic tree were predicted and analyzed.

284 ngle nucleotide polymorphism (SNP) analysis, phylogenetic trees were assembled to determine relatedne

285 Phylogenetic trees were characterized by two distinct fe

286 Intragenotypic phylogenetic trees were constructed for each viral gene

287 Phylogenetic trees were generated using the maximum like

288 Phylogenetic trees were inferred using maximum likelihoo

289 Phylogenetic trees were then generated for humans, rats,

290 (PfAgo) belongs to a different branch in the phylogenetic tree, which is most closely related to that

291 Our results demonstrate that inferring phylogenetic trees while accounting for dependent site e

292 eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the mult

293 y assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP.

294 posed TUP method is more capable of building phylogenetic trees with a stronger biological support.

295 y higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune esc

296 Phylogenetic trees with hundreds of thousands of leaves

297 ruct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a giv

298 etric method for estimating distributions of phylogenetic trees, with the goal of identifying trees t

299 sample rooted networks and the embedding of phylogenetic trees within networks.

300 is supports a similar model, although a full phylogenetic tree would be required to definitively dete