diff --git a/README.md b/README.md index 1730c65..c8916a2 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ -piqtree2 is a library which allows you use IQ-TREE directly from Python! +`piqtree2` is a library which allows you use IQ-TREE directly from Python! The interface with python is through [cogent3](https://cogent3.org) objects, as shown below. ## Note @@ -31,8 +31,12 @@ tree = build_tree(aln, "JC", rand_seed=1) # Optionally specify a random seed. print("Tree topology:", tree) # A cogent3 tree object print("Log-likelihood:", tree.params["lnL"]) +# In a Jupyter notebook, try tree.get_figure() to see a dendrogram ``` +> **Note** +> See the [cogent3 docs](https://cogent3.org) for examples on what you can do with cogent3 trees. + ### Fit Branch Lengths to Tree Topology ```python @@ -85,4 +89,4 @@ tree3 = make_tree("(a,b,(d,(c,e)));") pairwise_distances = robinson_foulds(tree1, tree2, tree3) # Supports any number of trees (for a sequence of trees use *seq_of_trees) print(pairwise_distances) # A numpy array containing pairwaise Robinson-Foulds distances between trees -``` \ No newline at end of file +```