faq.md
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

FAQ

Which tree file formats are supported? Newick (.nwk, .tre, .treefile), Nexus (.nexus, .nex), PhyloXML (.xml), and multi-tree files such as BEAST .trees. See get_supported_extensions and read_tree_auto.

My tip labels contain no taxonomy. Can Rclade still work? Yes. Provide an external two-column taxonomy file via taxonomy_file (or taxonomy_file in plot_timetree). See read_taxonomy_file and summarize_taxonomy_quality_with_file.

I got a "non-monophyletic group" warning. What does it mean? The taxonomic group you asked to collapse is not monophyletic — its members do not share a single MRCA. By default Rclade warns and skips it. Set strict = TRUE to abort instead. Use check_monophyly to investigate.

How do I change the time unit (Ma vs Ga)? Set unit = "Ma" or unit = "Ga" in plot_timetree. If NULL, Rclade infers it from the edge-length magnitude.

Can I use a circular layout with a timescale? The timescale works best with layout = "rectangular". For circular layouts, set add_timescale = FALSE, or use timescale_mode = "linear" to draw a linear timescale axis.

How do I cite Rclade? Use the citation("Rclade") command, or the CITATION file shipped with the package. Also see save_session_info() to record the exact environment.

The plot is slow / the tree is huge. Use show_tip_label = FALSE, prefer space_mode = "proportional", and consider low_memory = TRUE. For many trees, use batch_plot.

I got a "label(s) exceed 500 characters ... truncated" warning. What happened? ape's Newick parser aborts the whole R process on Linux for labels longer than ~512 characters, so Rclade truncates labels over 500 characters to 400 characters + a _RCLADE_TRUNC suffix before parsing. If your labels must match an external taxonomy file or sequence IDs exactly, shorten them upstream.

How do I run Rclade non-interactively (HPC / pipeline)? Use run_rclade_cli from a shell, or call plot_timetree() / batch_plot() inside a script. Redirect logs with set_log_file.

My file has multiple trees and I get an error. Set multi_tree_mode to "first", "last", "random", or "all" (or "split" in batch mode) to control which tree(s) to use.

Where is the full function reference? Reference index lists all functions by module (26 of them exported via NAMESPACE), each with a usage example.

中文文档在哪里？ 中文文档位于 docs/cn/，入口为 docs/cn/index.md。