Man pages for guerreror/pepo
Estimate Hemiplasy and Homoplasy on a Phylogeny
| branch_k2 | Calculate the length of a branch that ends with coalescence... |
| branch_k3 | Calculate branch lengths in genealogy that involves ILS |
| branch_length_correlation | Correlation between number of substitutions and coalescent... |
| calc_hrf | Calculate the Hemiplasy Risk Factor in a three-species clade. |
| convert_from_cf | Use concordance factors as approximate branch lengths |
| fix_mpest_tips | Change values of branch lengths at tips |
| homoplasy_mutations | Get probabilities of mutation along all branches |
| pepo | P(e)P(o): Compute the relative importance of hemiplasy and... |
| pr_double_hit | Calculate probability of two mutations on three-species tree |
| prep_branch_lengths | Prepare branches for HRF calculation |
| pr_hemiplasy | Probability of incongruence due to hemiplasy in a... |
| pr_homoplasy | Probability of incongruence due to homoplasy in a... |
| pr_mutation | Calculate the probability of at least one mutation on a... |
| tomato | Phylogeny of 36 nightshade accessions. |
| to_phylo4d | Convert to 'phylo4' class |
| to_treedata | Convert to 'treedata' |
| tree_hrf | Calculate HRF for all branches on a tree |
