| タイトル |
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ja
直接最適化法 direct optimization の問題点
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en
Problems in direct optimization
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| 作成者 |
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| アクセス権 |
open access |
| 主題 |
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Other
en
direct optimization
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Other
en
POY
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Other
en
ILD
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Other
en
DNA sequence
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Other
en
alignment
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Other
en
phylogeny
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Other
en
homology
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NDC
486
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| 内容注記 |
-
Abstract
en
Problems in direct optimization method as implemented in the software POY were reviewed. Alignment of highly variable regions using POY is problematic because it likely provides artificial maximization of pseudo-homology within the alignment. If the variable regions are aligned with conserved regions, then the bias could be emerged in two ways. When the conserved regions contain only weak phylogenetic signal, then stochastic similarities within the variable regions strongly affect to the final alignment. This type of bias can be emerged even if the variable regions are aligned independently. As a result, aligned variable sequences may provide superior amount of pseudo-signal which could even mask true weak signal contained in the conserved regions. When the conserved regions contain significant phylogenetic signal, then the variable regions will play as adherents of the conserved data even if the variable regions contain no or even contradicting phylogenetic signal. The adherent bias is especially problematic when data set contains heterogeneous sequences by gene introgression, recombination, or lineage sorting. Structure- or similarity-based approaches should be used in aligning DNA sequences.
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| 出版者 |
ja
日本動物分類学会
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| 日付 |
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| 言語 |
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| 資源タイプ |
journal article |
| 出版タイプ |
AM |
| 資源識別子 |
HDL
http://hdl.handle.net/2115/56458
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| 関連 |
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| 収録誌情報 |
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PISSN
1342-2367
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NCID
AN1056362X
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ja
タクサ : 日本動物分類学会誌
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巻30
開始ページ17
終了ページ29
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| ファイル |
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| コンテンツ更新日時 |
2023-07-26 |
