msaevaluation

This repository includes the scripts implemented for the Multiple Sequence Evaluation Project conducted at the Department of Computer Science in the University of Illinois at Urbana-Champaign.

Here is a brief description of the folders. For more detailed information, please refer to the related folder's readme file.

1) EasyMethodsRunningScripts:

    This folder includes the scripts for running the following alignment methods:
    
    Mafft variants, Promals, ContrAlign, ProbAlign, ProbCons, Muscle,
    Prime, Clustal-Omega, DiAlign, KAlign, and Prank
    
2) IntensiveMethodsRunningScripts:

    This folder includes a sample script for running computationally intensive methods 
	(i.e., BAli-Phy, TCoffee, and Mafft-Homologs) on different benchmarks using an HPC platform.
	
3) Plotting:

	The scripts used for plotting the material in the article.
	
4) MikesThoroughFiles:

	Mike will have to remove these files along with this line of documentation after he downloads them.

Here are the references and a link to the published article:

TBD

For more information, please do not hesitate to contact us through the following email:

warnow [at] illinois [dot] edu