Our conservation index application combines several estimation methods applied to the conservation computation process with parallelization and divide-and-conquer techniques substantially improving its performance without affecting its accuracy.
The software is available here.
To generate a basic report file of the conversation analysis, for a DNA alignment applying the unweighted entropy method and detecting CI greater than 0.99, run:
$ python3.4 generate_report.py -if align.fasta -st dna -rt basic -fm unweighted -cm entropy -co greater -th 0.99
To generate a detailed report file of the conversation analysis, for a protein alignment applying the weighted variance method and detecting CI less than 0.5, run:
$ python3.4 generate_report.py -if align.fasta -st protein -rt detailed -fm weighted -cm variance -co less -th 0.5
Any question or support request should be addressed to: zaramit at googlegroups dot com