FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3037977384> ?p ?o ?g. }

• W3037977384 endingPage "462" @default.
• W3037977384 startingPage "440" @default.
• W3037977384 abstract "Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several best practices for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming]." @default.
• W3037977384 created "2020-07-02" @default.
• W3037977384 creator A5033195125 @default.
• W3037977384 creator A5081119038 @default.
• W3037977384 date "2020-08-14" @default.
• W3037977384 modified "2023-10-12" @default.
• W3037977384 title "Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?" @default.
• W3037977384 cites W1748508858 @default.
• W3037977384 cites W1889423108 @default.
• W3037977384 cites W1924404512 @default.
• W3037977384 cites W1963957860 @default.
• W3037977384 cites W1988783684 @default.
• W3037977384 cites W2007234533 @default.
• W3037977384 cites W2012196076 @default.
• W3037977384 cites W2021883973 @default.
• W3037977384 cites W2033339460 @default.
• W3037977384 cites W2056251063 @default.
• W3037977384 cites W2066289589 @default.
• W3037977384 cites W2069093933 @default.
• W3037977384 cites W2069567328 @default.
• W3037977384 cites W2092672051 @default.
• W3037977384 cites W2097065253 @default.
• W3037977384 cites W2100990361 @default.
• W3037977384 cites W2102502076 @default.
• W3037977384 cites W2108039804 @default.
• W3037977384 cites W2114833586 @default.
• W3037977384 cites W2115556561 @default.
• W3037977384 cites W2115888213 @default.
• W3037977384 cites W2116103312 @default.
• W3037977384 cites W2119641595 @default.
• W3037977384 cites W2119837484 @default.
• W3037977384 cites W2122302865 @default.
• W3037977384 cites W2124682384 @default.
• W3037977384 cites W2125024684 @default.
• W3037977384 cites W2127322768 @default.
• W3037977384 cites W2127359962 @default.
• W3037977384 cites W2127556561 @default.
• W3037977384 cites W2127774996 @default.
• W3037977384 cites W2127860913 @default.
• W3037977384 cites W2128016314 @default.
• W3037977384 cites W2132926880 @default.
• W3037977384 cites W2141052558 @default.
• W3037977384 cites W2145562754 @default.
• W3037977384 cites W2147461064 @default.
• W3037977384 cites W2151320514 @default.
• W3037977384 cites W2152293390 @default.
• W3037977384 cites W2152688507 @default.
• W3037977384 cites W2159957100 @default.
• W3037977384 cites W2160378127 @default.
• W3037977384 cites W2162336040 @default.
• W3037977384 cites W2164541345 @default.
• W3037977384 cites W2167770609 @default.
• W3037977384 cites W2174889714 @default.
• W3037977384 cites W2175367716 @default.
• W3037977384 cites W2176256193 @default.
• W3037977384 cites W2179623716 @default.
• W3037977384 cites W2187860865 @default.
• W3037977384 cites W2258865027 @default.
• W3037977384 cites W2263985547 @default.
• W3037977384 cites W2277574918 @default.
• W3037977384 cites W2277953252 @default.
• W3037977384 cites W2308452887 @default.
• W3037977384 cites W2323303653 @default.
• W3037977384 cites W2338402689 @default.
• W3037977384 cites W2342704856 @default.
• W3037977384 cites W2549209567 @default.
• W3037977384 cites W2610523845 @default.
• W3037977384 cites W2739198517 @default.
• W3037977384 cites W2748256387 @default.
• W3037977384 cites W2756194227 @default.
• W3037977384 cites W2765571775 @default.
• W3037977384 cites W2793555634 @default.
• W3037977384 cites W2796277430 @default.
• W3037977384 cites W2797930545 @default.
• W3037977384 cites W2801132017 @default.
• W3037977384 cites W2883695758 @default.
• W3037977384 cites W2890156100 @default.
• W3037977384 cites W2942952185 @default.
• W3037977384 cites W2951147603 @default.
• W3037977384 cites W2951890991 @default.
• W3037977384 cites W2952299127 @default.
• W3037977384 cites W2962714894 @default.
• W3037977384 cites W2972445055 @default.
• W3037977384 cites W2979671820 @default.
• W3037977384 cites W3014064997 @default.
• W3037977384 cites W3038057260 @default.
• W3037977384 cites W4231969088 @default.
• W3037977384 cites W4378646759 @default.
• W3037977384 doi "https://doi.org/10.1093/sysbio/syaa064" @default.
• W3037977384 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32797207" @default.
• W3037977384 hasPublicationYear "2020" @default.
• W3037977384 type Work @default.
• W3037977384 sameAs 3037977384 @default.
• W3037977384 citedByCount "24" @default.
• W3037977384 countsByYear W30379773842020 @default.
• W3037977384 countsByYear W30379773842021 @default.
• W3037977384 countsByYear W30379773842022 @default.
• W3037977384 countsByYear W30379773842023 @default.

• next