Rename MANUAL.txt to MANUAL.md
Started fixing MD.
Rename INSTALL.txt to INSTALL.md
Update INSTALL.md
Fixed some MD, so that it renders well
Update errorhandle.py

added meaningful error code when a module was not found
Fixed runtime error bug for PE lib and empty repeat.fa file bug
Merge branch 'hotfix/1.1.1'
The networkx package was updated to return a generator from connected_component_subgraphs. This caused len() to fail. Updated code to reflect this.
Merge pull request #7 from fadern/develop

Develop
Merge pull request #6 from rchikhi/patch-1

Update errorhandle.py
Merge pull request #5 from jvhaarst/master

Moved INSTALL.txt and MANUAL.txt to MarkDown versions