diff --git a/README.md b/README.md index 88ba736..4355f29 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,7 @@ Note that TreeCluster can run within seconds even on ultra-large datasets, so it ## Usage ```bash -usage: TreeCluster.py [-h] [-i INPUT] -t THRESHOLD [-s SUPPORT] - [-m METHOD] +usage: TreeCluster.py [-h] [-i INPUT] -t THRESHOLD [-s SUPPORT] [-m METHOD] [-tf THRESHOLD_FREE] optional arguments: -h, --help show this help message and exit @@ -24,6 +23,9 @@ optional arguments: Clustering Method (options: avg_clade, length, length_clade, max, max_clade, med_clade, root_dist, single_linkage_clade) (default: max_clade) + -tf THRESHOLD_FREE, --threshold_free THRESHOLD_FREE + Threshold-Free Approach (options: argmax_clusters) + (default: None) ``` ## Clustering Methods @@ -71,5 +73,8 @@ optional arguments: 3. Leaves cannot be connected by branches with support below *s* * For a tree with *n* leaves, this algorithm is O(*n*) +## Threshold-Free Approaches +* **Argmax Clusters:** Choose the threshold that maximizes the number of non-singleton clusters over all thresholds from 0 to *t* + ## Requirements * [Biopython](http://biopython.org/)