File	Date	Author	Commit
Dependencies	2014-09-30	unknown	[e7bb65] Initial commit
SequencePad.py	2014-09-30	unknown	[0b1966] Adding licence. Please do not abuse prior commi...
aliglarge.txt	2014-09-30	unknown	[e7bb65] Initial commit
aligsmall.txt	2014-09-30	unknown	[e7bb65] Initial commit
readme.txt	2014-09-30	unknown	[e7bb65] Initial commit

Read Me

9/29/2014 - SequencePad beta release 

This sequence alignment editor is part of the SPADE software suite.

This is a limited release of the core functionality that includes:

Selection - click and drag to select a region. Right-click to save as a group.
Motion - turn on through the Options menu. Click and drag to manually edit.
Color by type - cyan:hydrophobic, red:negative, yellow:positive, orange: polar.
Wrap/unwrapped views - adjust in the Options menu.
Open File - Currently supports alignments with residue single-letter-codes only.

Future work includes:

Double buffering with a limited graphics update model.
Motion will move Group objects as groups.
Feature histograms under blocks of code or between wrapped sections.
Incorporation into SPADE sequence and structure alignment GUIs. 
More coloring schemes.

Known problems include:

Turning on scrollbars interferes with current geometry construction.
Slow performance with large alignments.
Sub-optimal performance with click-and-drag motion.
Save alignment doesn't work.