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Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks ( Quercus section Quercus )

https://doi.org/10.1139/gen-2016-0202
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1112s47openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.ympev.2013.02.002openalex-snapshot
Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.0904867106openalex-snapshot
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inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/bts482openalex-snapshot
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu121openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btw352openalex-snapshot
RADIS:analysis ofRAD-seq data for interspecific phylogeny
inferredcites →https://doi.org/10.1093/molbev/msn185openalex-snapshot
Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects
inferredcites →https://doi.org/10.1093/molbev/msu325openalex-snapshot
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inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
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inferredcites →https://doi.org/10.1093/sysbio/syt032openalex-snapshot
Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)
inferredcites →https://doi.org/10.1093/sysbio/syw036openalex-snapshot
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inferredcites →https://doi.org/10.1098/rspb.2017.0300openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.111120.110openalex-snapshot
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
inferredcites →https://doi.org/10.1111/1755-0998.12378openalex-snapshot
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inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05730.xopenalex-snapshot
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inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
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inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.12023openalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.12155openalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.12228openalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.13269openalex-snapshot
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inferredcites →https://doi.org/10.1111/mec.13457openalex-snapshot
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inferredcites →https://doi.org/10.1186/1471-2105-13-s19-s15openalex-snapshot
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inferredcites →https://doi.org/10.1186/1471-2164-9-488openalex-snapshot
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inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0019315openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0033394openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0093975openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0140175openalex-snapshot
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inferredcites →https://doi.org/10.1534/g3.116.030411openalex-snapshot
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inferredcites →https://doi.org/10.3732/apps.1400042openalex-snapshot
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ece3.4122openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11295-019-1372-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11676-020-01288-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s13595-018-0705-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s40725-018-0076-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ympev.2017.11.003openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107731openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msac119openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msac278openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syaa081openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2022.06.21.496980openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/823641openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jse.12433openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jse.12580openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jse.12724openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jse.12928openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/mec.14869openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/mec.16459openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/mec.16816openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.14773openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.14951openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.16162openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.16274openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12676openalex-snapshot
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inferred← citeshttps://doi.org/10.1139/gen-2017-0155openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12859-022-04790-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fgene.2020.00742openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ani11082226openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/f12060786openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/f12070882openalex-snapshot
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inferred← citeshttps://doi.org/10.6084/m9.figshare.20115327openalex-snapshot
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inferred← citeshttps://doi.org/10.64898/2026.05.14.725274openalex-snapshot
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inferred← citeshttps://doi.org/10.64898/2026.06.09.730892openalex-snapshot
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