Mathematical Hierarchies and Biology最新文献

The performance of the neighbor-joining method of phylogeny reconstruction 系统发育重建邻接法的性能

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/08

K. Atteson

引用次数: 20

Estimation of missing distances in path-length matrices: Problems and solutions 路径长度矩阵中缺失距离的估计:问题与解决方法

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/12

P. Landry, F. Lapointe

引用次数: 11

Multiple trees: Fitting two or more tree structures to proximity data 多树:将两个或多个树结构拟合到邻近数据中

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/22

J. Carroll, G. Soete

引用次数: 1

Phylogeny graphs of arbitrary digraphs 任意有向图的系统发育图

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/15

F. Roberts, Li Sheng

引用次数: 11

Complexity issues in hierarchical optimization 层次优化中的复杂性问题

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/13

P. Pardalos, X. Deng

引用次数: 7

Krohn-Rhodes theory, hierarchies & evolution Krohn-Rhodes理论，等级制度和进化

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/02

Chrystopher L. Nehaniv, J. Rhodes

引用次数: 2

Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages 从多态特征推断进化树，以及对印欧语系的分析

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/03

Maria Luisa Bonet, C. Phillips, T. Warnow, Shibu Yooseph

引用次数: 1

Concerning the NJ algorithm and its unweighted version, UNJ 关于NJ算法及其非加权版本，UNJ

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/09

O. Gascuel

{"title":"Concerning the NJ algorithm and its unweighted version, UNJ","authors":"O. Gascuel","doi":"10.1090/dimacs/037/09","DOIUrl":"https://doi.org/10.1090/dimacs/037/09","url":null,"abstract":"In this paper we will present UNJ, an unweighted version of the NJ algorithm (Saitou and Nei 1987; Studier and Keppler 1988). We will demonstrate that UNJ is well suited when the data are of the ( ) ( ) δ ε ij ij ij d = + type, where ( ) d ij is a tree distance, and when the εij are independent and identically distributed noise variables. Simulations confirm this theory. On a more general level, we will study the three main components of the agglomerative approach, applied to the reconstruction of tree distances. (i) We will demonstrate that the selection criterion for the pair to be agglomerated, used by NJ and UNJ, retains its meaning whatever the variances and covariances of the δij estimates. We will also provide a new proof of the correction of this criterion, based on an interpretation in acentrality terms proposed by Mirkin (1996). (ii) Using the results of Vach (1989), of which we will provide a simple new demonstration, we propose an analytical formula which enables the correct least-squares estimation of edge lengths in ( ) O n time, where n is the number of objects. (iii) We will provide a class of admissible reduction formulae which guarantee the finding of the true tree with additive data. We propose to choose, among these formulae, the minimum variance reduction, so that at each step we use estimates which are as reliable as possible in choosing the pair to be agglomerated. We will present the general solution, and apply it to the particular data model retained here.","PeriodicalId":336874,"journal":{"name":"Mathematical Hierarchies and Biology","volume":"50 4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116707563","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: 137

Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees 基因树与物种树比较的方法有注释复制、树作图和复制

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/05

O. Eulenstein, B. Mirkin, M. Vingron

引用次数: 16

Nesticity

Mathematical Hierarchies and Biology Pub Date : 1900-01-01 DOI: 10.1090/dimacs/037/14

Pierre Hansen, D. D. Werra

引用次数: 0