کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
5918993 1570808 2015 12 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک بوم شناسی، تکامل، رفتار و سامانه شناسی
پیش نمایش صفحه اول مقاله
Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
چکیده انگلیسی


• An implementation of IterPCR (Pol and Escapa, 2009) is now available in TNT.
• It uses a simple and fast method for checking triplets (LSI or PC).
• The method is much faster than Phyutility (Smith and Dunn, 2008).
• LSI in RogueNaRok (Aberer et al., 2013) is much slower because it uses quartets.
• The optimality criterion in RogueNaRok may fail to detect problematic taxa.

This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead of the O(t3) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.

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ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Molecular Phylogenetics and Evolution - Volume 88, July 2015, Pages 93–104