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 patients were more widely distributed in the phylogenetic tree.

3 according to their relationships in plants' phylogenetic tree.

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

5 geographic movements along the branches of a phylogenetic tree.

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

7 he pulvinar is consistent across the primate phylogenetic tree.

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

9 mily, while simultaneously inferring a dated phylogenetic tree.

10 on to incorporate annotations throughout the phylogenetic tree.

11 demics, and constructed a maximum likelihood phylogenetic tree.

12 ing in unsequenced branches of the microbial phylogenetic tree.

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

14 sion in sensitivity to herbicides within the phylogenetic tree.

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

16 efined the basal portion of the Y chromosome phylogenetic tree.

17 olutionary processes along the branches of a phylogenetic tree.

18 ts derived from placing them on a calibrated phylogenetic tree.

19 torial constraints defined by the underlying phylogenetic tree.

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

21 each of these intervals we inferred a local phylogenetic tree.

22 , however, tend to blur the structure of the phylogenetic tree.

23 rality of these structural motifs across the phylogenetic tree.

24 different Conus species were used to build a phylogenetic tree.

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

26 rior distribution is designed to utilize the phylogenetic tree.

27 ral different approaches being used to infer phylogenetic tree.

28 e corresponding transmission clusters from a phylogenetic tree.

29 tribution of consciousness across the animal phylogenetic tree.

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

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

32 expansion or loss occurred on the angiosperm phylogenetic tree.

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

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

35 the interpretation of the relationship among phylogenetic trees.

36 or experimental design and reconstruction of phylogenetic trees.

37 pled from rates of speciation as measured on phylogenetic trees.

38 relationship among a large set of competing phylogenetic trees.

39 rt and maximum genetic distance within large phylogenetic trees.

40 rium that could not have been observed using phylogenetic trees.

41 e in nature and confound characterization of phylogenetic trees.

42 t aims to find MFASTs in sets of many, large phylogenetic trees.

43 reement subtrees (MFASTs) in a collection of phylogenetic trees.

44 and has been studied using both fossils and phylogenetic trees.

45 quence alignments, hidden Markov models, and phylogenetic trees.

46 olving power of ITS towards earlier nodes of phylogenetic trees.

47 lysed using multiple sequence alignments and phylogenetic trees.

48 approaches from ancestor-descendant pairs to phylogenetic trees.

49 ikelihood and Bayesian analyses yield robust phylogenetic trees.

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

51 elationships within OGs based on analysis of phylogenetic trees.

52 ods are well suited for constructing massive phylogenetic trees.

53 cten sequences of various species to build a phylogenetic tree, (2) examined cten mRNA levels in huma

54 , which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology an

55 Phylogenetic tree also showed close relationship of RbTI

56 However, phylogenetic tree analysis further revealed monotypic vi

57 Structural alignment and phylogenetic tree analysis indicate that StnA represents

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

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

60 It is ubiquitous across the phylogenetic tree and is broadly classified into three c

61 of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or

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

63 Phylogenetic tree and synteny analyses of trout and othe

64 that could delineate sublineages within the phylogenetic tree and that could be used as potential bi

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

66 , but tools that facilitate visualization of phylogenetic trees and associated environmental data hav

67 roblem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from

68 Both phylogenetic trees and networks are typically reconstruc

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

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

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

72 Efforts to reconstruct phylogenetic trees and understand evolutionary processes

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

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

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

76 ting the number of duplication events on the phylogenetic tree, and that maximum likelihood and weigh

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

78 gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and betw

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

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

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

82 Phylogenetic trees are used to analyze and visualize evo

83 usters corresponded to major clusters in the phylogenetic tree as well, it seems a plausible hypothes

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

85 In addition, we provide local phylogenetic trees as an alternate visualization to asse

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

87 The phylogenetic tree based on the receptor-determining regi

88 We built phylogenetic trees based on genomic sequences of functio

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

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

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

92 A phylogenetic tree built from BovB sequences from species

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

94 We constructed a phylogenetic tree by comparing single-nucleotide polymor

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

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

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

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

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

100 r these results demonstrate that approximate phylogenetic trees can be produced in the absence of mul

101 Phylogenetic trees can be used to infer the processes th

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

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

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

105 A resulting phylogenetic tree consisted of four sublineages and indi

106 A phylogenetic tree consisted of two evolutionarily distin

107 f individuals fall in different positions in phylogenetic trees constructed from sequences from oppos

108 estingly, amino acid sequence comparison and phylogenetic tree construction clustered the newly isola

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

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

111 uence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and seq

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

113 cker and Cluster Matcher can rapidly process phylogenetic trees containing tens of thousands of seque

114 A phylogenetic tree could also be constructed directly fro

115 However, phylogenetic trees demonstrate extensive mixing of virus

116 n of endonucleases from one clade within the phylogenetic tree demonstrates strong conservation of pr

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

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

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

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

121 that can assess the quality and stability of phylogenetic tree estimates and identify the most reliab

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

123 multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative

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

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

126 Moreover, coalescence times of the phylogenetic tree follow a coalescence process.

127 in clostridial phylogeny, we have compared a phylogenetic tree for a concatenated set of 50 widesprea

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

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

130 , by combining data from a field study and a phylogenetic tree for Mojave Desert rodents to address p

131 on of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

132 A phylogenetic tree for the extant Hawaiian honeycreepers

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

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

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

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

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

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

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

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

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

142 widely used for over three decades to infer phylogenetic trees from molecular data.

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

144 t methods from the literature and also build phylogenetic trees from them.

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

146 Analyses of phylogenetic trees generated by cgMLST displayed a high

147 Central to the resource are phylogenetic trees generated from structurally informed

148 The phylogenetic trees generated from these loci show simila

149 In phylogenetic trees, GlyT2-like sequences from invertebra

150 The phylogenetic tree had three major branches: one with the

151 able, bromodomains from other regions of the phylogenetic tree have shallower pockets.

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

153 ned sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally de

154 Although the use of phylogenetic trees in epidemiological investigations has

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

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

157 rer supports the visualization of very large phylogenetic trees, including features such as the autom

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

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

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

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

162 yote, Geobacter sulfurreducens, and employed phylogenetic tree inference for LTTR classification.

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

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

165 kov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum li

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

167 proaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene.

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

169 Phylogenetic trees inferred from core-genome single nucl

170 Phylogenetic trees inferred from mitochondrial genes ret

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

172 Here, a phylogenetic tree is constructed for the thymidine kinas

173 on of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization

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

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

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

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

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

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

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

181 The phylogenetic trees map out the evolutionary route taken

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

183 r evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and sta

184 Phylogenetic trees now include inference of horizontal t

185 A phylogenetic tree of all sampled tilapia was generated u

186 bacterial strains distributed throughout the phylogenetic tree of cyanobacteria.

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

188 existing structural types with the putative phylogenetic tree of human languages, four conclusions m

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

190 and FADY) were present in both species; in a phylogenetic tree of microsomal FAD enzymes, FADX and FA

191 rn primates, in conjunction with an accurate phylogenetic tree of relatedness, has the power to chart

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

193 tes the number of covarying mutations on the phylogenetic tree of the aligned sequences into the cova

194 tailed tree-building models, the base of the phylogenetic tree of the Herpesviridae family has been e

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

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

197 possible to locate 165 TE insertions in the phylogenetic tree of the three genomes/subgenomes.

198 mily has been reported in agnathans, but the phylogenetic tree of the Y1 subfamily is not yet clear.

199 We derive a dated phylogenetic tree of this proposed superfamily with a ti

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

201 Phylogenetic trees of DNA sequences of a group of specim

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

203 Phylogenetic trees of emrE grouped YSLPVs with algae, su

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

205 Heavy- and light-chain phylogenetic trees of identified 10E8 variants displayed

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

207 Heavy- and light-chain phylogenetic trees of PGT141-145 somatic variants also d

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

209 FFP-based phylogenetic trees of seven gastric Helicobacter species

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

211 PhyLAT uses a known phylogenetic tree on the species in the multiple alignme

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

213 s capable of parsing common file formats for phylogenetic trees, performing basic transformations and

214 Our dated phylogenetic tree places Macrauchenia as sister to Peris

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

216 Phylogenetic trees provide important insights into mecha

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

218 narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader one

219 Phylogenetic tree reconciliation is a widely used method

220 Maximum parsimony phylogenetic tree reconciliation is an important techniq

221 Phylogenetic trees reconstructed from molecular sequence

222 defines operational taxonomic units based on phylogenetic tree reconstruction and dynamic clustering

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

224 Phylogenetic tree reconstruction methods relying on this

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

226 We utilized phylogenetic tree reconstructions and comparative genomi

227 jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity

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

229 A robust multiprotein phylogenetic tree reflects the major human migration out

230 Furthermore, the phylogenetic tree representations are not unique for any

231 Here, we reconstruct a genus-level molecular phylogenetic tree representing the 20,000 species found

232 Phylogenetic trees revealed a close relationship between

233 interrogate and visualise variation within a phylogenetic tree setting.

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

235 The phylogenetic tree showed a strong temporal-spatial struc

236 The phylogenetic tree showed country-specific correlation wi

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

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

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

240 Phylogenetic trees simulated with the recently reported

241 C into programs that calculate quantities on phylogenetic tree structures is straightforward, so the

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

243 urrent best approach for generating a single phylogenetic tree, suitable for use as a reference phylo

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

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

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

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

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

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

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

251 o identify the origin of a QTL allele on the phylogenetic tree that relates the taxa.

252 data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, sh

253 ata we demonstrate that this method produces phylogenetic trees that are more accurate than other com

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

255 In a phylogenetic tree, the BIS amino acid sequences from app

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

257 description of past events in the form of a phylogenetic tree; the nodes and leaves of which are sta

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

259 unction over large sequence databases, using phylogenetic trees to extrapolate from the relatively sp

260 mplete linkage clustering algorithm to build phylogenetic trees to indicate how the distances among t

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

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

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

264 A Bayesian phylogenetic tree, together with associated dating analy

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

266 tion orders, using only interaction data and phylogenetic tree topology, which are significantly corr

267 dy mass changes along individual branches of phylogenetic trees using an adaptive peak model of evolu

268 We established phylogenetic trees using hematopoietic colonies.

269 We constructed phylogenetic trees using these variants, or subsets of t

270 mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison a

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

272 A phylogenetic tree was constructed with 19 604 Swiss sequ

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

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

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

276 For each phylogenetic tree we identified strains sharing a leaf n

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

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

279 By constructing phylogenetic trees, we identified 2 to 5 subgenotype all

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

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

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

283 Phylogenetic trees were characterized by two distinct fe

284 Phylogenetic trees were constructed based on common repl

285 Intragenotypic phylogenetic trees were constructed for each viral gene

286 Phylogenetic trees were generated using the maximum like

287 Phylogenetic trees were inferred using maximum likelihoo

288 Phylogenetic trees were pre-constructed for each gene ca

289 Phylogenetic trees were then generated for humans, rats,

290 ence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel)

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

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 aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignme

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