Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

@article{Feng2007ProgressiveSA,
  title={Progressive sequence alignment as a prerequisitetto correct phylogenetic trees},
  author={D. F. Feng and Russell F. Doolittle},
  journal={Journal of Molecular Evolution},
  year={2007},
  volume={25},
  pages={351-360}
}
SummaryA progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison… Expand
Progressive alignment and phylogenetic tree construction of protein sequences.
TLDR
The preliminary set of pair wise measurements reveals any sub clusters that may exist in the set, which can be treated as units during the alignment process, ensuring that the relative positions of the residues within the cluster will not be altered. Expand
Event-based Phylogeny Inference and Multiple Sequence Alignment
TLDR
The final algorithm is a novel tool that suggests a complete evolution hypothesis of input sequences, consisting of a phylogeny and of the placement of mutations on the edges of the resulting tree. Expand
Improving Kalign via Reconstruction of Phylogenetic Tree and Iteration
  • Fan Yang, Qingxin Zhu, Mingyuan Zhao
  • Computer Science
  • 2009 WRI World Congress on Computer Science and Information Engineering
  • 2009
TLDR
An iterative algorithm, which combines re-estimation of distance and reconstruction of phylogenetic tree, is introduced to refine the alignment created by Kalign, and shows that the algorithm achieves more accurate alignment than Kalign does. Expand
Simultaneous statistical multiple alignment and phylogeny reconstruction.
TLDR
This paper presents and discusses a strategy based on simulated annealing, which makes use of the TKF2 model to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences'indel history, i.e., their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree. Expand
Progressive multiple sequence alignment with indel evolution
TLDR
A new dynamic programming algorithm to align two MSAs –represented by the underlying homology paths– by full maximum likelihood under PIP in polynomial time, and apply it progressively along a guide tree, which is the first polynometric time progressive aligner with a rigorous mathematical formulation of indel evolution. Expand
Alignment-free Phylogeny Reconstruction Based On Quartet Trees
TLDR
This thesis developed Multi-SpaM, a novel alignment-free approach that tries to combine the best of both worlds for phylogeny reconstruction and showed multiple ways that could help to improve Multi- SpaM. Expand
Multiple sequence alignment accuracy and evolutionary distance estimation
TLDR
The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods, which has implications for choosing new taxa and genomes to sequence when resources are limited. Expand
Phylogenetic and genomic analysis
This chapter briefly discusses the different steps in constructing evolutionary trees, including collecting data sets of homologous sequences, generating a multiple-sequence alignment, inferring treeExpand
REVIEW Multiple Sequence Alignment in Phylogenetic Analysis
Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since theExpand
Efficient Construction of accurate Multiple alignments and Large-Scale phylogenies
TLDR
The first part of the dissertation describes a new algorithm that dramatically increases the speed and scalability of a common method for phylogeny inference called neighbor-joining, implemented in a new tool, called NINJA, which is more than an order of magnitude faster than a very fast implementation of the canonical algorithm. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 51 REFERENCES
Estimating the reliability of evolutionary trees.
TLDR
Six protein sequences from the same 11 mammalian taxa were used to estimate the accuracy and reliability of phylogenetic trees using real, rather than simulated, data and it was concluded that it is possible to give a reasonable estimate of the reliability of the final tree, at least when several sequences are combined. Expand
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
TLDR
An integrated method is proposed that generates both an alignment of a set of sequences and a phyletic tree and is applied to the analysis of the evolution of 5S rRNA sequences in prokaryotes. Expand
Aligning amino acid sequences: Comparison of commonly used methods
SummaryWe examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of “weighting” in order to determine which approach is most sensitiveExpand
Accuracy of estimated phylogenetic trees from molecular data
TLDR
A comparison of the accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data was examined by using computer simulation, and it is shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained. Expand
Simultaneous comparison of three protein sequences.
TLDR
The algorithm is an extension of the method developed by S. Needleman and C. Wunsch, but it decreases the almost prohibitively long computing time required by a direct naive extension to a practical level: it takes time proportional to the cube of the mean sequence length, in comparison to the fifth power time taken by the direct extension. Expand
A strategy for sequence phylogeny research
TLDR
A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods. Expand
A practical method for calculating evolutionary trees from sequence data.
TLDR
This paper describes another method, related to the previous one, in which a present-day sequence can serve temporarily as an ancestor for purposes of determining the evolutionary tree regardless of the rates of evolution of the sequences involved. Expand
The phylogeny of human globin genes investigated by the maximum parsimony method
TLDR
Gene phylogenetic trees were constructed by the maximum parsimony method for various sets of ninety six globin chain amino acid sequences spanning plant and animal kingdoms and provided evidence for the hominoid affinities of the gibbon and the close phyletic relationship of the African apes to man. Expand
Further improvements in the method of testing for evolutionary homology among proteins.
  • W. Fitch
  • Biology, Medicine
  • Journal of molecular biology
  • 1970
TLDR
An earlier method for detecting significant genetic relatedness between two gene products is improved upon through three specific measures, which modifies the log likelihood-ratio test to permit one to estimate the probability that a presumptive homologous relationship could be a chance event. Expand
A method for the simultaneous alignment of three or more amino acid sequences
TLDR
An algorithm for the concurrent comparison of three or more amino acid sequences that is a progressive evaluation of selected segments from each sequence, which has the advantage of being both rapid and minimally consumptive of computer memory when constructing an alignment. Expand
...
1
2
3
4
5
...