A small number of tools for handling data from IQtree runs. In particular to facilitate the analysis of ancestral state transitions predicted by IQTree.

Currently there are two tools:

1. parse_state_file/state_to_nibble
2. extract_transitions/extract_transitions

The first of these is used to extract the most likely ancestral states from IQTree .state files and extant sequences into a more compact nibble representation. The second tool uses the files output by state_to_nibble along with the .treefile produced by IQTree to count the transitions at each node.

Both tools are in development and may be changed in the future.

For documentation see the README.md files and the source code.

Both tools make use of functions from klib. In particular extract_transitions makes use of knhx.h and knhx.h to parse the tree.