Man pages for svteichman/TreeVizPackage
Tree Visualization Package
| alignments_to_cat | Makes new folder with alignments Makes a new folder with... |
| check_missingness | Check missingness Compute the proportion of missingness for... |
| check_support | Check support Check the proportion of trees that support... |
| compute_geodesic | Geodesic implementation Calculates the geodesic distance... |
| compute_logmap | Compute logmap Compute the logmap centered at one tree for... |
| count_topologies | Count topologies Count number of distinct topologies present... |
| genes_missing_outgroup | Finds missing genes Provides a subset of genes from a list... |
| geodesic_MDS | Geodesic implementation Calculates the geodesic distance... |
| get_target_genes | Lists genes without missingness Takes a list of genes and... |
| list_long_branch_tips | List long branch tips Returns a list of tips that are... |
| perform_MDS | Classical MDS of six difference tree distances Performs... |
| perform_smacof | Distance MDS of six difference tree distances Performs... |
| plot_boot_support | Plot bootstrap support Plot a tree with bootstrap support... |
| plot_gene_support | Plot gene tree support Plot a tree with gene tree support... |
| plot_logmap | Plot logmap Plot logmap coordinates using the first two... |
| plot_MDS | Plots MDS results Plots MDS results of trees for each... |
| plot_node_value | Plot node value Plot a tree with node values on each internal... |
| plot_support | Plot support Plot a tree with support values on each internal... |
| recode_long_branch | Recode long branches Returns a phylo or multiphylo object... |
| recode_outgroup | Recodes outgroup edge. Recodes the branch going to an... |
| remove_empty_lines | Removes empty lines Removes empty lines from a fasta file (so... |
| remove_genomes | Removes genomes Removes genome lines from a fasta file. |
| rename_labs | Rename labels Given a set of old and new labels, switch... |
| scale_MDS | Scales MDS results Scales MDS results of trees for each... |
