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4,067
Multiple sequence alignment with the Clustal series of programs
 Nucleic Acids Res
, 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
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Cited by 747 (5 self)
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the robustness, portability and userfriendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI
PAML: a program package for phylogenetic analysis by maximum likelihood
 COMPUT APPL BIOSCI 13:555–556
, 1997
"... PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the tr ..."
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Cited by 1459 (17 self)
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among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
Activity recognition from userannotated acceleration data
, 2004
"... In this work, algorithms are developed and evaluated to detect physical activities from data acquired using five small biaxial accelerometers worn simultaneously on different parts of the body. Acceleration data was collected from 20 subjects without researcher supervision or observation. Subjects ..."
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Cited by 515 (7 self)
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. Subjects were asked to perform a sequence of everyday tasks but not told specifically where or how to do them. Mean, energy, frequencydomain entropy, and correlation of acceleration data was calculated and several classifiers using these features were tested. Decision tree classifiers showed the best
ModelBased Analysis of Oligonucleotide Arrays: Model Validation, Design Issues and Standard Error Application
, 2001
"... Background: A modelbased analysis of oligonucleotide expression arrays we developed previously uses a probesensitivity index to capture the response characteristic of a specific probe pair and calculates modelbased expression indexes (MBEI). MBEI has standard error attached to it as a measure of ..."
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Cited by 775 (28 self)
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Background: A modelbased analysis of oligonucleotide expression arrays we developed previously uses a probesensitivity index to capture the response characteristic of a specific probe pair and calculates modelbased expression indexes (MBEI). MBEI has standard error attached to it as a measure
A New Statistical Parser Based on Bigram Lexical Dependencies
, 1996
"... This paper describes a new statistical parser which is based on probabilities of dependencies between headwords in the parse tree. Standard bigram probability estimation techniques are extended to calculate probabilities of dependencies between pairs of words. Tests using Wall Street Journal ..."
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Cited by 490 (4 self)
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This paper describes a new statistical parser which is based on probabilities of dependencies between headwords in the parse tree. Standard bigram probability estimation techniques are extended to calculate probabilities of dependencies between pairs of words. Tests using Wall Street
Loopy belief propagation for approximate inference: An empirical study. In:
 Proceedings of Uncertainty in AI,
, 1999
"... Abstract Recently, researchers have demonstrated that "loopy belief propagation" the use of Pearl's polytree algorithm in a Bayesian network with loops can perform well in the context of errorcorrecting codes. The most dramatic instance of this is the near Shannonlimit performanc ..."
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Cited by 676 (15 self)
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. Introduction The task of calculating posterior marginals on nodes in an arbitrary Bayesian network is known to be NP hard In this paper we investigate the approximation performance of "loopy belief propagation". This refers to using the wellknown Pearl polytree algorithm [12] on a Bayesian network
Arb: A software environment for sequence data
 Nucleic Acids Res
, 2004
"... The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed ..."
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Cited by 421 (10 self)
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phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, pro®le and ®lter calculation, phylogenetic analyses, speci®c hybridization probe design
Distance Browsing in Spatial Databases
, 1999
"... Two different techniques of browsing through a collection of spatial objects stored in an Rtree spatial data structure on the basis of their distances from an arbitrary spatial query object are compared. The conventional approach is one that makes use of a knearest neighbor algorithm where k is kn ..."
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Cited by 390 (21 self)
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Two different techniques of browsing through a collection of spatial objects stored in an Rtree spatial data structure on the basis of their distances from an arbitrary spatial query object are compared. The conventional approach is one that makes use of a knearest neighbor algorithm where k
Accelerating Parallel Maximum Likelihoodbased Phylogenetic Tree Calculations using Subtree Equality Vectors
 In Proceedings of SC2002
, 2002
"... Heuristics for calculating phylogenetic trees for a large sets of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. ..."
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Cited by 15 (8 self)
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Heuristics for calculating phylogenetic trees for a large sets of aligned rRNA sequences based on the maximum likelihood method are computationally expensive.
AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method, Proc
 IEEE Comput. Soc. Bioinform. Conf
"... Heuristics for the NPcomplete problem of calculating the optimal phylogenetic tree for a set of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. In most existing algorithms the tree evaluation and branch length optimization functions, calculating the l ..."
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Cited by 12 (5 self)
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Heuristics for the NPcomplete problem of calculating the optimal phylogenetic tree for a set of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. In most existing algorithms the tree evaluation and branch length optimization functions, calculating
Results 1  10
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