AlignDist - hacking the alignment distance
https://github.com/novadam/AlignDist
 
 
### INTRODUCTION ###

AlignDist is a collection of tools for working with alignment distances. Currently features the following two programs:

AlignDistCalc is a program for mass-evaluation of test alignments against a reference. It supports standard FASTA files and StatAlign mpd/log files both as test and reference.

AlignDistSample takes samples approximately uniformly from the set of alignments that are at a given distance from a reference alignment. It uses the Metropolis coupled MCMC (parallel tempering) technique to allow efficient sampling. Also features a temperature tuning mode where chain temperatures are automatically adjusted to meet the prescribed chain swap acceptance ratios.

The alignment distance measure in use by these tools are defined in the paper:
Schwartz et al. (2005) Alignment Metric Accuracy, arXiv:q-bio/0510052


### USAGE ###

To get help:

java -jar adcalc.jar -h
java -jar adsample.jar -h


Example (typical) usage:

1. AlignDistCalc

java -jar adcalc.jar ref.fsa test1.fsa test2.fsa

2. AlignDistSample

java -jar adsample.jar -a=0.8 ref.fsa


### LICENSE ###

AlignDist is distributed under the GNU General Public License Version 3. A copy of the license is found in LICENSE.