Evolutionary Bioinformatics Online最新文献_第10页

The Role of the Phylogenetic Diversity Measure, PD, in Bio-informatics: Getting the Definition Right 系统发育多样性测量，PD，在生物信息学中的作用:得到正确的定义

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200008

D. Faith

引用次数: 59

Gaussian Quadrature Formulae for Arbitrary Positive Measures 任意正测度的高斯正交公式

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200010

A. Fernandes, W. Atchley

引用次数: 27

LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates From Molecular Phylogenies 激光:从分子系统发育中检测多样化率的时间变化的最大可能性工具包

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200024

D. Rabosky

引用次数: 322

Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges 系统发育多样性(PD)与生物多样性保护:一些生物信息学挑战

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200007

D. Faith, A. Baker

{"title":"Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges","authors":"D. Faith, A. Baker","doi":"10.1177/117693430600200007","DOIUrl":"https://doi.org/10.1177/117693430600200007","url":null,"abstract":"Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bioinformatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socioeconomic data.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121937786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 387

Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make 总证据、平均共识和简约的矩阵表示:距离的差异

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200018

Claudine Levasseur, F. Lapointe

引用次数: 14

Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances 基于距离的系统发育方法中的拓扑偏差:遗传距离过高和过低的问题

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200034

X. Xia

引用次数: 14

Using minimum bootstrap support for splits to construct confidence regions for trees 使用最小引导支持分割来构建树的置信区域

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200030

E. Susko

{"title":"Using minimum bootstrap support for splits to construct confidence regions for trees","authors":"E. Susko","doi":"10.1177/117693430600200030","DOIUrl":"https://doi.org/10.1177/117693430600200030","url":null,"abstract":"Many of the estimated topologies in phylogenetic studies are presented with the bootstrap support for each of the splits in the topology indicated. If phylogenetic estimation is unbiased, high bootstrap support for a split suggests that there is a good deal of certainty that the split actually is present in the tree and low bootstrap support suggests that one or more of the taxa on one side of the estimated split might in reality be located with taxa on the other side. In the latter case the follow-up questions about how many and which of the taxa could reasonably be incorrectly placed as well as where they might alternatively be placed are not addressed through the presented bootstrap support. We present here an algorithm that finds the set of all trees with minimum bootstrap support for their splits greater than some given value. The output is a ranked list of trees, ranked according to the minimum bootstrap supports for splits in the trees. The number of such trees and their topologies provides useful supplementary information in bootstrap analyses about the reasons for low bootstrap support for splits. We also present ways of quantifying low bootstrap support by considering the set of all topologies with minimum bootstrap greater than some quantity as providing a confidence region of topologies. Using a double bootstrap we are able to choose a cutoff so that the set of topologies with minimum bootstrap support for a split greater than that cutoff gives an approximate 95% confidence region. As with bootstrap support one advantage of the methods is that they are generally applicable to the wide variety of phylogenetic estimation methods.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126436594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Genome Halving with an Outgroup 与外群体的基因组减半

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200028

Chunfang Zheng, Qian Zhu, D. Sankoff

引用次数: 33

Modelling prokaryote gene content 模拟原核生物基因含量

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200029

M. Spencer, E. Susko, A. Roger

{"title":"Modelling prokaryote gene content","authors":"M. Spencer, E. Susko, A. Roger","doi":"10.1177/117693430600200029","DOIUrl":"https://doi.org/10.1177/117693430600200029","url":null,"abstract":"The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126884505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 23

Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden 基于结构序列聚结和贝叶斯MCMC推理的群体参数估计

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200026

G. Ewing, A. Rodrigo

引用次数: 15