updated readme and docs

README.md

@@ -17,11 +17,11 @@ It serves as the backend for the web application [eMap](https://emap.bu.edu/), a
 # Installation
 
 ### Pip
-Pip installation will only install python dependencies, and requires [Graphviz](https://graphviz.gitlab.io/) in order to work. This is sufficient to run PyeMap analysis and view graph images, but some features will be missing.
+Pip installation will only install python dependencies, This is sufficient to run PyeMap analysis and view graph images, but some features will be missing.
 ```
 pip install pyemap
 ```
-For full functionality, install [RDKit](https://www.rdkit.org/docs/Install.html), [MUSCLE](https://www.drive5.com/muscle/), [MSMS](http://mgltools.scripps.edu/packages/MSMS) (not available on Mac OS Catalina and later), and [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html), all of which can be downloaded free of charge from their owners, and are available on most platforms. 
+For full functionality, install [RDKit](https://www.rdkit.org/docs/Install.html), [Graphviz](https://graphviz.gitlab.io/),  [PyGraphviz](https://pygraphviz.github.io/), [MUSCLE](https://www.drive5.com/muscle/), [MSMS](http://mgltools.scripps.edu/packages/MSMS) (not available on Mac OS Catalina and later), and [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html), all of which can be downloaded free of charge from their owners, and are available on most platforms. 
 
 # Getting started
 Please see our tutorials for [single](https://pyemap.readthedocs.io/en/latest/tutorial/single_protein.html) and [multiple](https://pyemap.readthedocs.io/en/latest/tutorial/mining.html) protein analysis to help get started using PyeMap. We also provide sample Jupyter notebooks in the examples directory.

docs/install.rst

@@ -4,8 +4,8 @@ PyeMap officially supports Python versions 3.7 and later, and has been tested fo
 
 **Pip**
 
-Pip installation will only install python dependencies, and requires a working Graphviz_ installation.
-This is sufficient to run PyeMap analysis, but some features will be missing::
+Pip installation will only install python dependencies. This is sufficient to run PyeMap analysis, 
+but some features will be missing::
 
     $ pip install pyemap
 
@@ -15,6 +15,8 @@ For full functionality, install the following packages:
     - MSMS_: residue depth criterion for surface exposed residues (not available on MacOS Catalina)
     - DSSP_: solvent accessibility criterion for surface exposed residues
     - MUSCLE_: Multiple sequence alignment
+    - Graphviz_: visualization of graphs
+    - PyGraphviz_ : visualization of graphs
 
 All of these packages can be downloaded free of charge from their respective owners, and build recipes are available on the
 Anaconda_ cloud for some platforms.
@@ -23,6 +25,7 @@ Anaconda_ cloud for some platforms.
 .. _MSMS: http://mgltools.scripps.edu/packages/MSMS
 .. _DSSP: https://github.com/cmbi/xssp/releases
 .. _Graphviz: https://graphviz.gitlab.io/
+.. _Pygraphviz: https://pygraphviz.github.io/
 .. _RDKit: https://www.rdkit.org/docs/Install.html
 .. _MUSCLE: http://www.drive5.com/muscle/
 .. _RCSB: https://www.rcsb.org/