Preprocessed gene trees from "Xenolog Classification"
Data CreatorDarby, Charlotte
Relation (Is Referenced By)https://doi.org/10.1093/bioinformatics/btw686
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CitationDarby, Charlotte; Stolzer, Maureen; Ropp, Patrick; Barker, Daniel; Durand, Dannie. (2016). Preprocessed gene trees from "Xenolog Classification", [dataset]. https://doi.org/10.7488/ds/1503.
DescriptionPreprocessed gene trees from 49 taxa of Cyanobacteria and 16 Proteobacteria used by Darby et al. (2017, Bioinformatics 33:640-649; doi:10.1093/bioinformatics/btw686) are provided here. These consist of trees for 13623 of the gene families of Latysheva et al. (2012, doi:10.1093/bioinformatics/bts008). Using Notung-220.127.116.11 (Stolzer et al. 2012, doi:10.1093/bioinformatics/bts386), unrooted trees with bootstrap support (out of 200; doi:10.7488/ds/1485) were preprocessed with the following steps: (1) root with DTL (duplication, transfer, loss) model --costdup 3 --costtrans 2.5 --costloss 2; (2) rearrange with DL model --costdup 3 --costloss 2 --threshold 90%; (3) reroot with DTL model --costdup 3 --costtrans 2.5 --costloss 2. Both zip files contain the output from this pipeline. The Newick format trees reflect the tree topology after this process. The Notung format trees also include the reconciliation, and other meta data. The Notung format is described in detail in Appendix A (File Formats) of the Notung manual (http://www.cs.cmu.edu/~durand/Notung). ## Acknowledgment ## This work was funded by the National Science Foundation grant DBI-1262593. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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