Merge branch 'master' into phylogenetic_tree

# Conflicts:
#	ghosttree/filter.py
#	ghosttree/scaffold/hybridtree.py
#	ghosttree/scaffold/tests/test_hybridtree.py
#	setup.cfg

README.rst

@@ -19,6 +19,14 @@ files available here
 
 The most recent ghost-trees we've created are in our tree repository.
 
+If you use ghost-tree in published research, please cite our `software 
+publication in Microbiome <https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0153-6>`_. Thank you!
+
+J. Fouquier, J.R. Rideout, E. Bolyen, J. Chase, A. Shiffer, D. McDonald, 
+R. Knight, J.G. Caporaso, and S.T. Kelley. ghost-tree: creating hybrid-gene 
+phylogenetic trees for diversity analysis. Microbiome. 
+(February 2016) DOI: 10.1186/s40168-016-0153-6
+
 Using ghost-tree.nwk files for your analyses:
 =============================================
 
@@ -53,10 +61,6 @@ You should then have your filtered .biom table, a ghost-tree.nwk, and a mapping
 file, which will then allow you to use `beta_diversity_through_plots.py <http://qiime.org/scripts/beta_diversity_through_plots.html>`_
 in QIIME.
 
-If you had any trouble, please email jennietf@gmail.com.
-I am also interested in improving documentation, so please let me know if you
-find errors or have suggestions! Thank you!
-
 Developers:
 ===========
 
@@ -97,7 +101,15 @@ using the command line tool, see our `ghost-tree .ipynb workflow <https://github
 
 This project is currently under active development and may evolve without notice. So, please
 update your local repository, and check here for changes. If you're interested in
-contributing, please contact `@JTFouquier <https://github.com/JTFouquier>`__.
+contributing, please contact `@JTFouquier <https://github.com/JTFouquier>`_.
+
+Help:
+=====
+
+If you have any trouble, please email jennietf@gmail.com. I am happy to help! :)
+
+I am also interested in improving documentation, so please let me know if you
+find errors or have suggestions!
 
 .. |Build Status| image:: https://travis-ci.org/JTFouquier/ghost-tree.svg?branch=master
    :target: https://travis-ci.org/JTFouquier/ghost-tree

ghosttree/filter.py

@@ -25,9 +25,9 @@ def filter_positions(alignment_fh, maximum_gap_frequency,
 
 def _filter_gap_positions(aln, maximum_gap_frequency):
 
-    aln_gap_frequencies = (aln.gap_frequencies(axis='sequence',
-                                               relative=False) /
-                           aln._seqs.count())
+    aln_gap_frequencies = (aln.gap_frequencies(
+                           axis='sequence',
+                           relative=False) / aln._seqs.count())
     aln_gap_frequencies_boolean = (aln_gap_frequencies <=
                                    maximum_gap_frequency)
     aln = aln.iloc[:, aln_gap_frequencies_boolean]

setup.cfg

@@ -1,4 +1,4 @@
 [flake8]
 filename = *.py
 exclude = *.pyc, __pycache__
-ignore=E722
+ignore = E722