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A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalianSOX-3origin of the testis-determining geneSRY

Kazutaka Katoh, Takashi Miyata
1999 FEBS Letters  
This also suggests that the optimum tree corresponds to the global optimum in tree topology space and thus probably coincides with the ML tree inferred by intact ML analysis.  ...  All different iterative processes started from 100 independent initial trees ultimately converged on one optimum tree with the largest log-likelihood value, suggesting that a limited number of initial  ...  Slowly evolving SRY sequences were used for tree inference, except for human sequence.  ... 
doi:10.1016/s0014-5793(99)01621-x pmid:10601652 fatcat:hlnugukqhnfejpzfzqe5ga73ri

Optimum alphabetic binary trees [chapter]

T. C. Hu, J. D. Morgenthaler
1996 Lecture Notes in Computer Science  
We describe a modi cation of the Hu{Tucker algorithm for constructing an optimal alphabetic tree that runs in O(n) time for several classes of inputs.  ...  We also give simple conditions and a linear algorithm for determining, in some cases, if two adjacent nodes will be combined in the optimal alphabetic tree.  ...  Conclusion We have shown that a modi cation of the Hu{Tucker algorithm will run in linear time for many classes on input sequences.  ... 
doi:10.1007/3-540-61576-8_86 fatcat:c6gmlxa7r5hfpmjtndodq7fecu

Page 434 of Compendium : Continuing Education for Veterinarians Vol. 12, Issue 3 [page]

1990 Compendium : Continuing Education for Veterinarians  
Likewise, the cli- nician needs to know how much the probability of a favor- able outcome of a suboptimum sequence would have to im- prove before it would have the same value as the optimum sequence.  ...  The clini- cian needs to know by what amount the cost of a subopti- mum therapy would have to be reduced before it would be equal in value to the optimum sequence.  ... 

A Class of Reduced-Complexity Viterbi Detectors for Partial Response Continuous Phase Modulation

A. Svensson, C. Sundberg, T. Aulin
1984 IEEE Transactions on Communications  
From [5] it is known that the phase tree given by the optimum g R ( t ) pulse approximates the 3RC phase tree very well.  ...  This phase tree is shown in Fig. 5 , where the 4RC phase tree is also given (dashed) . The loss at h = 1/2 compared to the optimum 4RC receiver is about 0.35 dB.  ... 
doi:10.1109/tcom.1984.1095967 fatcat:45gtnqzanrabvmy24nuea6csgq

Characterizing Local Optima for Maximum Parsimony

Ellen Urheim, Eric Ford, Katherine St. John
2016 Bulletin of Mathematical Biology  
optimum quickly.  ...  When Nearest Neighbor Interchange (NNI) operations are used, multiple local optima can occur even for "perfect" sequence data, which results in hill-climbing searches that never reach a global optimum.  ...  multiple local optima even for sequences that are compatible with exactly one tree, SPR-treespaces have a single local optimum.  ... 
doi:10.1007/s11538-016-0174-0 pmid:27234257 fatcat:h4lypshx6vdhlflg2a43ibby6a

Systematic exploration of guide-tree topology effects for small protein alignments

Fabian Sievers, Graham M Hughes, Desmond G Higgins
2014 BMC Bioinformatics  
However, default guide-trees fall way short of the optimum attainable scores.  ...  Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments.  ...  optimum tree shape.  ... 
doi:10.1186/1471-2105-15-338 pmid:25282640 pmcid:PMC4287568 fatcat:zfzyrnh6mfcndmi6ixbhnnpqim

Trajectory and Policy Aware Sender Anonymity in Location Based Services [article]

Alin Deutsch, Richard Hull, Avinash Vyas, Kevin Keliang Zhao
2012 arXiv   pre-print
We show that optimum TP-aware anonymization is computationally harder than snapshot P-aware anonymization (NP-complete vs. PTIME).  ...  Thus finding the optimum quad-tree policy that uses cloak sequences from T to anonymize a set U of trajectories is equivalent to finding the optimum configuration C of the tree T w.r.t. U .  ...  a quad-tree of quad-cloak sequences.  ... 
arXiv:1202.6677v1 fatcat:ty572lyncje6zifkuvvowawhca

Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees

P. W. Purdom, P. G. Bradford, K. Tamura, S. Kumar
2000 Bioinformatics  
Motivation: In the maximum parsimony (MP) method, the tree requiring the minimum number of changes (discrepancy) to explain the given set of DNA or amino acid sequences is chosen to represent their evolutionary  ...  We propose a single column discrepancy heuristic which increases this cost by predicting a minimum additional discrepancy needed to attach the sequences yet to be added to the partial phylogenetic-tree  ...  Suppose that for an optimum phylogenetic tree the following situation is true for each column of the data.  ... 
doi:10.1093/bioinformatics/16.2.140 pmid:10842736 fatcat:43o6m2uwnjbebgcj72zxeij7ne

On the Best Evolutionary Rate for Phylogenetic Analysis

Ziheng Yang, D. Cannatella
1998 Systematic Biology  
DNA sequence data were sim ulated usin g bo th ® xed tre es w ith spe ci® ed branch len gths and random trees w ith branch len gths generated from a m odel of clado genesis.  ...  In this study, I use com puter simulations to study the effect of the evolutionary rate on the accuracy of phy logeny reconstruction and to quantify the optimum levels of sequence diverge nce.  ...  There were no noticeable differences in the optimum tree lengths am ong the m etho ds; in p articular, the optimum tree length for p arsim ony is not any sm aller than those for the likelihoo d m etho  ... 
doi:10.1080/106351598261067 pmid:12064232 fatcat:7lht3fku7rfi7lvv4gk3vwdlzm

Page 35 of Journal of Systems Management Vol. 20, Issue 6 [page]

1969 Journal of Systems Management  
Of course, we must recall that we have found an optimum job sequence when its make- span is no greater than any of the unbranched- from nodes in the tree.  ...  different job sequences and 1: n+n(n-1) n! nodes in the entire tree. In particular, for our problem, this means that there are 24 different job sequences, and 65 nodes in the entire tree.  ... 

Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?

Amelia B Bellamy-Royds, Marcel Turcotte
2007 BMC Bioinformatics  
We then explore the relative successes of different approaches to designing the tree that will guide progressive alignments of sequence profiles to create a multiple alignment and prediction of conserved  ...  However, we have also discovered that the amount of detail included in a consensus structure prediction is highly dependent on the order in which sequences are added to the alignment (the guide tree),  ...  above optimum [5] .  ... 
doi:10.1186/1471-2105-8-190 pmid:17559658 pmcid:PMC1904245 fatcat:nlmoqtusdfeexmmm2ugkuymiru

Finding an optimum edit script between an XML document and a DTD

Nobutaka Suzuki
2005 Proceedings of the 2005 ACM symposium on Applied computing - SAC '05  
In this paper, we consider finding K optimum edit scripts between an XML document and a regular tree grammar. We first prove that the problem is NP-hard.  ...  Finding optimum and near optimum edit scripts between an XML document and a schema is essential to correcting invalid XML documents.  ...  In fact, finding such a sequence leads to an optimum edit script for t n i , as explained later.  ... 
doi:10.1145/1066677.1066825 dblp:conf/sac/Suzuki05 fatcat:tabhsfkc6fh6tlwdaawjmlekae

SWAPSC: sliding window analysis procedure to detect selective constraints

M. A. Fares
2004 Bioinformatics  
The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and nonsynonymous nucleotide substitutions.  ...  Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints.  ...  SWAPSC slides the optimum window along the real sequence alignment and estimates the probability of K a and K s comparing each sequence with its ancestor inferred by maximum parsimony.  ... 
doi:10.1093/bioinformatics/bth303 pmid:15130925 fatcat:uwvk7lyxvzdozmyr4mucupnii4

SWAPSC: sliding window analysis procedure to detect selective constraints

M. A. Fares
2004 Computer applications in the biosciences : CABIOS  
The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and nonsynonymous nucleotide substitutions.  ...  Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints.  ...  SWAPSC slides the optimum window along the real sequence alignment and estimates the probability of K a and K s comparing each sequence with its ancestor inferred by maximum parsimony.  ... 
doi:10.1093/bioinformatics/bth329 pmid:15130925 fatcat:nbguf2pw3be2rbfn5kdwnk6fke

Phylogenetic analysis of large molecular data sets

Pamela S. Soltis, Douglas E. Soltis
2017 Botan‪ical Sciences  
a local optimum and the global optimum, and 3) the existence of multiple classes (islands) of most parsimonious trees.  ...  In this paper, we discuss several of these challenges, including 1) the failure of a search to find the most parsimonious trees (the local optimum) in a reasonable amount of time, 2) the difference between  ...  optimum.  ... 
doi:10.17129/botsci.1509 fatcat:km75wjqnrzgg3fr2v2aqwcoxky
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