[Biopython-dev] [Biopython (old issues only) - Bug #2815] (Closed) Bio.Application command line interfaces

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Sun Jul 24 22:16:56 UTC 2016

Issue #2815 has been updated by Markus Piotrowski.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

Commandline parser for MUSCLE has been merged to Biopython (ver. 1.5.1?)

Bug #2815: Bio.Application command line interfaces

* Author: Cymon J.
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
Attached is a module to run the MUSCLE alignment programme based on the Bio.Applications interface.

A couple of helper functions are included MuscleAlign and ProfileMuscleAlign. Discussion on the dev-list suggests that helper functions are superfluous. Maybe, but I thought I'd include them anyway. A couple of unittests are included for the helper funcs.


MuscleAlign.py (29.1 KB)
test_MuscleAlign.py (3.14 KB)
Applications.py (45.5 KB)
Applic.patch (1.45 KB)
TCoffeeCL.py (1.65 KB)

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