Man pages for Chien-Hsun/rePhylo
Re-investigating and Improving Phylogenies
| backboneBP | Summarize the Bootstrape Values of Backbone Nodes |
| barplotMulticf | Summarize 'cladeFilter' Result in Barplot |
| Brassidata | Single gene trees, a reference tree and a table of grouping... |
| cladeFilter | Filtering Sequences of Paralogy or With Other Misleading... |
| concor.node | Concordances of Trees with All Nodes of A Reference Tree |
| concor.trees | Analyze Concordances on Trees with All Groupings |
| createGrouping | Creating a Taxa Table as Input to Other Functions in package... |
| createUnref | createUnref |
| denominator | internal function |
| detect_closest_out_for_GD | Detect the existence of the closest outgroups for each gd |
| dot-check.concor | .check.concor |
| dot-cladefilter | .cladeFilter |
| dot-combine. | .combine. |
| dot-concor.node.unrooted | .concor.node.unrooted |
| dot-deno | internal function |
| dot-detect_out | Internal. Detect the existence of the closest outgroups for... |
| dot-filter_coverage | Internal. Filters the GD counts by the species coverage of... |
| dot-sum_sp_gd | Internal function |
| filter_GD_by_coverage | filters the GD counts by the species coverage of each of the... |
| make.idTable.phyto | generate node id table for the reference of phyto id and ape... |
| plot.cladeFilter | Plot 'cladeFilter' Result in 'trees' for One Grouping |
| plot.concor | Plot Concordances |
| plotFilteredGD | plot the gd result corrected by filter_GD_by_coverage and... |
| rewrite.tree | rewrite.tree |
| root_dist | internal function |
| select.backbone | internal function |
| summarizeMulticf | Summarize 'cladeFilter' Results with Multiple Groupings |
| summarize_sp_for_GD | Summarize number of species supporting gd |
