Search‐based optimization

Wheeler, Ward C.

doi:10.1111/j.1096-0031.2003.tb00378.x

Cited by 30 publications

(29 citation statements)

References 17 publications

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“…Simmons and Ochoterena (2000) discuss gap coding at length and provide several options for treating gaps. A search-based extension of fixed state optimization, not discussed here, is implemented in POY (Wheeler, 2003). Two papers (Wheeler 1999a;Lutzoni et al, 2000) independently addressed the inclusion of ambiguously aligned regions through a procedure called fragment-level alignment (Lee 2001; see Fig.…”

Section: Gaps and Data Exclusion Criteriamentioning

confidence: 99%

Opinions on Multiple Sequence Alignment, and an Empirical Comparison of Repeatability and Accuracy between POY and Structural Alignment

2007

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Section: Gaps and Data Exclusion Criteriamentioning

confidence: 99%

Opinions on Multiple Sequence Alignment, and an Empirical Comparison of Repeatability and Accuracy between POY and Structural Alignment

2007

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“…But this method, which partitions developmental sequences in paired events, suffers from strong methodological inconsistencies and can lead to erroneous results when it comes to phylogenetic tree reconstruction or optimization of hypothetical ancestors (Schulmeister and Wheeler ). Schulmeister and Wheeler () showed that whole developmental sequences could be used instead of paired events and proposed to analyze them as a single character (i.e., one developmental sequence is treated as a single multistate character in a search‐based optimization procedure—Wheeler ). This method necessitates, however, a pool of predetermined developmental sequences to reconstruct hypothetical ancestral sequences, and thus requires untestable assumptions.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic analyses of termite post‐embryonic sequences illuminate caste and developmental pathway evolution

Legendre

Whiting

Grandcolas

2013

Evolution and Development

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Termites are highly eusocial insects with a caste polyphenism (i.e., discontinuous morphological differences between castes) and elaborated behaviors. While the developmental pathways leading to caste occurrence are well-known in many species, the evolutionary origin of these pathways is still obscure. Recent molecular phylogenetic studies suggest multiple independent origins of sterile castes in termites, reviving a 30 years old debate. We demonstrate here that diploid sterile castes ("true" workers) evolved several times independently in this group and that this caste was lost at least once in a lineage with developmentally more flexible workers called pseudergates or "false" workers. We also infer that flexibility in post-embryonic development was acquired multiple times independently during termite evolution. We suggest that focusing on detailed developmental pathways in phylogenetic analyses is essential for elucidating the origin of caste polyphenism in termites.

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“…In particular, for the Hamming and Manhattan distance, to calculate all of the tree scores in the TBR neighborhood has time complexity O (| V | 3 ) [11]. For the GTAP however, it has time complexity O (| V | 4 ) [19,22-24], or O (| V | 3 ) by increasing the hidden factor from O ( n 2 ) to O ( n 3 ) (remember that typically n ≫| V |) [20,23]. …”

Section: The Algorithmsmentioning

confidence: 99%

Local search for the generalized tree alignment problem

Varón

Wheeler

2013

BMC Bioinformatics

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BackgroundA phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide. The problem of simultaneous tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the Generalized Tree Alignment Problem (GTAP). The GTAP is the Steiner Tree Problem for the sequence edit distance. Like many biologically interesting problems, the GTAP is NP-Hard. Typically the Steiner Tree is presented under the Manhattan or the Hamming distances.ResultsExperimentally, the accuracy of the GTAP has been subjected to evaluation. Results show that phylogenies selected using the GTAP from unaligned sequences are competitive with the best methods and algorithms available. Here, we implement and explore experimentally existing and new local search heuristics for the GTAP using simulated and real data.ConclusionsThe methods presented here improve by more than three orders of magnitude in execution time the best local search heuristics existing to date when applied to real data.

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Search‐based optimization

Cited by 30 publications

References 17 publications

Opinions on Multiple Sequence Alignment, and an Empirical Comparison of Repeatability and Accuracy between POY and Structural Alignment

Opinions on Multiple Sequence Alignment, and an Empirical Comparison of Repeatability and Accuracy between POY and Structural Alignment

Phylogenetic analyses of termite post‐embryonic sequences illuminate caste and developmental pathway evolution

Local search for the generalized tree alignment problem

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