Comprehensive phylogenomic inference of eucalypts reveals taxonomic limits through gene tree concordance

<p dir="ltr">This dataset contains 1,187 BUSCO alignments and their corresponding trees used in eucalypt phylogenomic inference. It also stores the results of taxonomic consistency test on individual tips across gene trees.</p><p><br></p><ul><li><code>metadata.tsv</code>: metadata of 1,024 eucalypt samples in the study</li><li><code>target_busco_CBA.fna</code>: CAPTUS target file for samples from CBA clade</li><li><code>target_busco_nonCBA.fna</code>: CAPTUS target file for samples from non-CBA clade</li><li><code>1024samples/</code>: output folders of the initial 1,024 eucalypt samples</li><li><ul><li><code>concatenated_1024samples.fna</code>: concatenated locus alignment</li><li><code>concatenated_ML_1024samples.treefile</code>: concatenated Maximum-Likelihood tree</li><li><code>locus_partition_1024samples.nex</code>: locus-based partition model and their substitution models</li><li><code>alltrees_1024samples.treefile</code>: all gene trees in Newick format</li><li><code>tct_subgenus_5n_1024samples.tsv</code>: per-sample subgenus consistency scores based on its 5 nearest neighbours</li><li><code>tct_section_5n_1024samples.tsv</code>: per-sample section consistency scores based on its 5 nearest neighbours</li></ul></li><li><code>701samples/</code>: output folders of the subsetted 701 eucalypt samples</li><li><ul><li><code>concatenated_701samples.fna</code>: concatenated locus alignment</li><li><code>concatenated_ML_CFs_701samples.treefile</code>: concatenated Maximum-Likelihood tree with gCF/sCF/qCF/bb/pp as branch labels</li><li><code>concatenated_ML_Ns_701samples.treefile</code>: concatenated Maximum-Likelihood tree with gN/sN/qN as branch labels</li><li><code>locus_partition_701samples.nex</code>: locus-based partition model and their substitution models</li><li><code>alltrees_701samples.treefile</code>: all gene trees in Newick format</li><li><code>tct_subgenus_Xn_701samples.tsv</code>: per-sample subgenus consistency scores based on its <code>X</code> nearest neighbours</li><li><code>tct_section_Xn_701samples.tsv</code>: per-sample section consistency scores based on its <code>X</code> nearest neighbours</li></ul></li></ul><p dir="ltr">All output files were generated using the <b>EucsPhylogenomics</b> pipeline (<a href="github.com/jeremiasivan/EucsPhylogenomics" target="_blank" rel="noreferrer">github.com/jeremiasivan/EucsPhylogenomics</a>), which also incorporates the <b>taxonomic consistency test</b> (<a href="github.com/jeremiasivan/TaxonomicConsistencyTest" target="_blank" rel="noreferrer">github.com/jeremiasivan/TaxonomicConsistencyTest</a>).</p>