Alignment Consensus Calculator

This program allows the user to calculate alignment conservation. It recognizes alignments in ClustalW format, and outputs a similarly formatted alignment where asterisks mark the alignment positions that have a user-inputted level of conservation.

The link to the jar file and the README are below. To download the jarfile, right-click the link and select 'download linked file' from the pull-down menu.

  1. README
  2. jarfile

An example of the usage for the Alignment Consensus Calculator is given below: 

java -jar alignments.jar -i cannabinoid.aln -c 80 > cannabinoid_80cons.aln
converts the original cannabinoid alignment file to a file where all positions with 80% conservation are marked with an asterisk.

Note that the filename (after the -i option) must correspond exactly to the name of the alignment file that you are using! You can leave out the redirection symbol (">") and the output filename (here "cannabinoid_80cons.aln"), and the output will go to STDOUT (i.e., to your terminal window).

The complete help file for this tool is: 

usage: edu.cornell.med.alignments.AlignmentConservation -i file [-c int] [-m char] [-h] 
 -i,--seqs 	The alignment input file. The format is ClustalW.
 -c,--cutoff 	User-defined marks will be printed below those
			columns that meet the conservation cutoff value.
			Default: 100
 -m,--mark 	The mark which will be printed below those columns
			that meet the conservation cutoff value. The default is an asterisk.
 -h,--help	Print this message
(Replace edu.cornell.med.alignments.AlignmentConservation with java -jar alignments.jar).

The source code for this project is available from the ICB SVN repository.