PersonalUtilities

This is a repository for several scripts used in a few studies.

• diversification_rate_sliding_window.middle.py was customized for Zhang SD, Jin JJ, et al. 2017. Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics. New Phytologist.

• TreePar.plot.R was customized for Zhang SD, Jin JJ, et al. 2017. Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics. New Phytologist.

• concatenate_fasta.py was first used in Zhang R, Wang YH, Jin JJ, et al. 2020. Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Systematic Biology

• get_annotated_regions_from_gb.py was first used in Zhang R, Wang YH, Jin JJ, et al. 2020. Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Systematic Biology

• Cluster_trees_by_bipartitions.py was customized for Zhang R, Wang YH, Jin JJ, et al. 2020. Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Systematic Biology

Some scripts were deprecated:

• plastome_arch_info.py was deprecated here and the alternative one was merged into GetOrganelle.