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. 2020 Nov 30;11:6096. doi: 10.1038/s41467-020-20005-6

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — Bar plots show the percentages of genes that are irreproducible when using IQ-TREE (in yellow) and RAxML-NG (in blue), respectively. The bar plot at the upper left is based on all 19,414 gene alignments from 15 phylogenomic data sets; it shows that the phylogenies of 3515/19,414 genes (18.11%) and 1813/19,414 genes (9.34%) are irreproducible between two replicates (Run1 and Run2) using IQ-TREE (in yellow) and RAxML-NG (in blue), respectively. The rest of the bar plots show the individual results for each of the 15 phylogenomic data sets. These data sets were constructed using five different but widely accepted gene sampling approaches (shown in parentheses): Ultraconserved Element (UCE) capture, Anchored Hybrid Enriched (AHE) capture, conserved exon capture, transcriptome sequencing, and whole-genome sequencing. All 77,656 analyses (19,414 alignments * 2 replicates * 2ML programs) were run using two threads per node on the Center for High-Throughput Computing (CHTC) at the University of Wisconsin-Madison. Detailed values are given in Supplementary Data 2. All gene alignments, gene trees, and log files, as well as statistics of the results, are available on the figshare repository: 10.6084/m9.figshare.11917770.