Adding copyright statement
Replacing the call to ic(), which has been removed, by a call to pssm.mean()
_recover_alignments does not use penalize_end_gaps
In pairwise2, allow penalize_end_gaps to be different for the two sequences
adding some description for penalize_end_gaps
Replacing tabs with spaces in C-code
Dont cast NULL pointers
Fix for Bug 3439. DR lines in SwissProt records don't have comments, so delete the code for splicing out comments from DR lines
Merge pull request #194 from pgarland/fix-3439

Fix for Bug 3439
Replace PyNumber_AsDouble by PyFloat_AsDouble, which does the same thing
Fixing a typo
Include directory is no longer needed for Bio.cpairwise2
Mention JASPER work and thank contibutors in NEWS file
Eric, Joao and Bow have also contributed to this release

Documentation change only, skip TravisCI [ci skip]
Improve Biopython installation with pip: avoid including numpy as dependency when automated. Instead explicitly avoid needing numpy installed to continue
Add helpful comment on pip dependency management
Brad worked on improving pip installation with virtual env
Add name length option for MAFFT
Thank Jian-Long Huang for MAFFT argument
Adding --phylipout to MAFFT wrapper