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

Discovery Environment Applications List

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Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML (http://svn.iplantcollaborative.org/iptol/Utils/Released/paml_run.pl) 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 http://de.iplantcollaborative.org/dl/d/D3E58B12-16A1-4953-9B3C-26D278D52995/codeml.ctl as control file,
stewart.aa from http://de.iplantcollaborative.org/dl/d/122ED453-B06B-4763-B616-91657548CB9B/stewart.aa as sequence data and
stewart.trees from http://de.iplantcollaborative.org/dl/d/2A8F9CFE-8D63-4EB0-B062-074C556B11D2/stewart.trees 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 (http://mirrors.iplantcollaborative.org/example_data/paml/mlc) as output file as well as Inf, rst, rst1, rub and ipc-####.ctl as intermediate result files.

Tool Source for App

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2 Comments

  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.