Collection of little scripts for doing stuff with phylogenetic trees.
| Script | Useful for you? | Description |
|---|---|---|
| add_nhx_tags | no | add nhx style tags to nodes mapping a gene tree to species tree labels. Good for Notung, but is hardcoded for my data. |
| annotate_tree | yes | add PAML tags to tree nodes for branch models |
| print_accessions | no | for getting info on taxa in tree from upstream data |
| symdiff_compare | yes | for comparing topology of one tree (usually ML tree) with several (often MCMC trees). adapted from the dendropy tutorial |
| symmdiff_table | yes | print table of all-by-all symmetric differences for a set of trees. Careful, not wise for lots of trees. Used in Liebeskind et al. 2012 |
| tree_map | no | replace names in tree with seq1,seq2 etc... |
| unique_trees | maybe | Get unique topologies from an MCMC sample |