The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

Maintenance: Tues, 28 Jan 2020


Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
User Portal                   8:00am to 5:00pm MST
The User Portal,, will be unavailable while we perform maintenance and updates.
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
Check your local timezone here 
Please contact for any questions, or concerns.






Skip to end of metadata
Go to start of metadata

Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML ( is a wrapper for Ziheng Yang's popular suite of programs in the package PAML. It can be used to run different phylogenetic analyses (e.d. estimating dN and dS or detecting branch and site-specific selection) in a maximum likelihood framework.

Quick Start

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > paml

Input File(s)

Use codeml.ctl from as control file,
stewart.aa from as sequence data and
stewart.trees from as tree file.

Import from URL to get the data into your Discovery Environment account.

Files are also located in the iPlant Community Data directory at the following path (type into the "viewing" box at the top of the data grid): /iplant/home/shared/iplantcollaborative/example_data/paml

Parameters Used in App

When the app is run in the Discovery Environment, use the default parameters with the above input file(s) to get the output provided in the next section below.

Output File(s)

Expect mlc ( as output file as well as Inf, rst, rst1, rub and ipc-####.ctl as intermediate result files.

Tool Source for App

  • No labels


  1. ☆☆☆☆☆ Links to example input files are dead. (by apepper)

  2. Thank you for letting us know (and apologies for the delay). The links have been updated.