MP-EST estimate species trees from a collection of gene trees by maximizing the pseudo-likelihood function. The input gene trees must be rooted trees. 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.