Conservation index

Description

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.

 

Download

The software is available here.

 

Documentation

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

There is a README document included in the download with all the documentation.
External software required: Python v3.4, BioPython v1.63+.

 

Contact

Any question or support request should be addressed to: zaramit at googlegroups dot com