UNF-PIPE/Tha-pipe — Issue #4: Multiple Alignment Parser
Author: simfor
Created: 2011-12-16 22:10:13+00:00
State: open

We need to parse the multiple alignment and look for oddities such as:
-Sequences differing substantially in length from the rest. This might indicate a frameshift or an incorrectly annotated gene.
-Poorly aligned sequences that we might have to remove altogether.
-Anything more?

We have to decide which output format the aligner should give. There are existing parsers for some formats such as XML. Maybe bioPerl has a Multiple Alignment Parser? Don't reinvent the wheel...