NJst estimate species trees from a collection of gene trees by a neighbor joining algorithm. The input gene trees could be rooted or unrooted trees, but the NJst tree is an unrooted species tree. Missing taxa are allowed in gene trees.

To estimate the species tree, users should put ML gene trees in a single tree file (download an example file genetrees.gt) and upload the tree file to the web server. To conduct a bootstrap analysis, users should put bootstrap gene tree files (one file per gene) in a folder and submit the folder as a zip file (download an example file bootstrap_genetrees.zip) to the web server.