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Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments

scientific article published on 08 October 2019

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title

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments (English)

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author name string

Marek Borowiec

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publication date

8 October 2019

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published in

Journal of Open Source Software

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volume

4

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issue

42

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page(s)

1635

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cites work

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

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Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

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Accounting for alignment uncertainty in phylogenomics

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Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

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Noisy: identification of problematic columns in multiple sequence alignments

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Pitfalls in supermatrix phylogenomics

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Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

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Contentious relationships in phylogenomic studies can be driven by a handful of genes.

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Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

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Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics

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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

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Multiple Sequence Alignment Accuracy and Phylogenetic Inference

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Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

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Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

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Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

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Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

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PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences

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(Q113307775)

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments

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