diff --git a/docs/content/faq.rst b/docs/content/faq.rst
index 27b4fe36a47fdee97b963856173697ad4c26121b..8c7046645de237ce9a6b961501151f4c8ccd82c8 100644
--- a/docs/content/faq.rst
+++ b/docs/content/faq.rst
@@ -5,10 +5,11 @@ FAQ
====================
Installation issues
- ====================
+====================
+--------------------------------------------------
Why am I getting all of these zlib errors?
-..........................................
+--------------------------------------------------
On certain operating systems (especially free Linux distributions) the complete
zlib libraries are not installed. Bedtools depends upon zlib in order to
@@ -37,3 +38,68 @@ and on Fedora/Centos this would be:
yum install zlib
yum install zlib1g-dev
+
+
+
+====================
+General questions
+====================
+
+
+--------------------------------------------------
+How do I know what version of bedtools I am using?
+--------------------------------------------------
+
+Use the --version option.
+
+.. code-block:: bash
+
+ $ bedtools --version
+ bedtools v2.17.0
+
+
+--------------------------------------------------
+How do I bring up the help/usage menu?
+--------------------------------------------------
+
+To receive a high level list of available tools in bedtools, use ```-h``:
+
+.. code-block:: bash
+
+ $ bedtools -h
+ bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
+ usage: bedtools <subcommand> [options]
+
+ The bedtools sub-commands include:
+
+ [ Genome arithmetic ]
+ intersect Find overlapping intervals in various ways.
+ window Find overlapping intervals within a window around an interval.
+ closest Find the closest, potentially non-overlapping interval.
+ coverage Compute the coverage over defined intervals.
+ map Apply a function to a column for each overlapping interval.
+ genomecov Compute the coverage over an entire genome.
+ merge Combine overlapping/nearby intervals into a single interval.
+ cluster Cluster (but don't merge) overlapping/nearby intervals.
+ complement Extract intervals _not_ represented by an interval file.
+ ...
+
+To display the help for a specific tool (e.g., ``bedtools shuffle``), use:
+
+.. code-block:: bash
+
+ $ bedtools merge -h
+
+ Tool: bedtools merge (aka mergeBed)
+ Version: v2.17.0
+ Summary: Merges overlapping BED/GFF/VCF entries into a single interval.
+
+ Usage: bedtools merge [OPTIONS] -i <bed/gff/vcf>
+
+ Options:
+ -s Force strandedness. That is, only merge features
+ that are the same strand.
+ - By default, merging is done without respect to strand.
+
+ -n Report the number of BED entries that were merged.
+ - Note: "1" is reported if no merging occurred.
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diff --git a/docs/content/installation.rst b/docs/content/installation.rst
index 6b6018fcad5c116112258e3effb055d3a421cce5..659c8db4eedd738adc8f23c335f502dad2e70270 100755
--- a/docs/content/installation.rst
+++ b/docs/content/installation.rst
@@ -2,12 +2,28 @@
Installation
############
+
``bedtools`` is intended to run in a "command line" environment on UNIX, LINUX
-and Apple OS X operating systems. Installing BEDTools involves downloading the
-latest source code archive followed by compiling the source code into binaries
-on your local system. The following commands will install ``bedtools`` in a
-local directory on an UNIX or OS X machine. Note that the **"<version>"**
-refers to the latest posted version number on http://bedtools.googlecode.com/.
+and Apple OS X operating systems. Installing ``bedtools`` involves either
+downloading the source code and compiling it manually, or installing stable
+release from package managers such as
+`homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_.
+
+
+
+
+--------------------------
+Installing stable releases
+--------------------------
+
+.....................................
+Compiling from source via Google Code
+.....................................
+
+Stable, versioned releases of bedtools are made available The following commands
+will install ``bedtools`` in a local directory on an UNIX or OS X machine.
+Note that the **"<version>"** refers to the latest posted version number
+on http://bedtools.googlecode.com/.
.. note::
@@ -27,3 +43,59 @@ your environment. You will typically require administrator (e.g. "root" or
"sudo") privileges to copy to ``usr/local/bin/``. If in doubt, contact you
system administrator for help.
+.....................................
+Installing with package managers
+.....................................
+
+In addition, stable releases of ``bedtools`` are also available through package
+managers such as `homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_,
+``apt-get`` and ``yum``.
+
+**Fedora/Centos**. Adam Huffman has created a Red Hat package for bedtools so
+that one can easily install the latest release using "yum", the Fedora
+package manager. It should work with Fedora 13, 14 and EPEL5/6 (
+for Centos, Scientific Linux, etc.).
+
+.. code-block:: bash
+
+ yum install BEDTools
+
+**Debian/Ubuntu.** Charles Plessy also maintains a Debian package for bedtools
+that is likely to be found in its derivatives like Ubuntu. Many thanks to
+Charles for doing this.
+
+.. code-block:: bash
+
+ apt-get install bedtools
+
+
+**Homebrew**. Carlos Borroto has made BEDTools available on the bedtools
+package manager for OSX.
+
+.. code-block:: bash
+
+ brew install bedtools
+
+
+
+-----------------------------
+Development versions
+-----------------------------
+
+The development version of bedtools is maintained in a Github
+`repository <https://www.github.com/arq5x/bedtools>`_. Bug fixes are addressed
+in this repository prior to release, so there may be situations where you will
+want to use a development version of bedtools prior to its being promoted to
+a stable release. One would either clone the repository with ``git``, as
+follows and then compile the source code as describe above:
+
+.. code-block:: bash
+
+ git clone https://github.com/arq5x/bedtools.git
+
+
+or, one can download the source code as a ``.zip`` file using the Github
+website. Once the zip file is downloaded and uncompressed with the ``unzip``
+command, one can compile and install using the instructions above.
+
+ .. image:: images/github-zip-button.png
diff --git a/docs/content/related-tools.rst b/docs/content/related-tools.rst
new file mode 100644
index 0000000000000000000000000000000000000000..71773be304c8e8b352c6aa989873aa268771825e
--- /dev/null
+++ b/docs/content/related-tools.rst
@@ -0,0 +1,56 @@
+##################
+Related software
+##################
+
+Bedtools has been used as an engine behind other genomics software and has been
+integrated into widely used tools such as Galaxy and IGV. Below is a likely
+incomplete list. If you know of others, please let us know, or better yet,
+edit the document on GitHub and send us a pull request. You can do this by
+clicking on the "Edit and improve this document" link in the lower lefthand
+corner.
+
+
+-------------------
+IGV
+-------------------
+Bedtools is now integrated into the IGV genome viewer as of IGV version 2.2. We
+are actively working withe IGV development team to improve and expand this
+integration. See
+`here <http://www.broadinstitute.org/igv/IGV2.2.x>`_
+and
+`here <https://www.broadinstitute.org/software/igv/bedtools>`_ for details.
+
+ .. image:: images/bedtoolsMenu.png
+
+-------------------
+Galaxy
+-------------------
+
+`Galaxy <https://main.g2.bx.psu.edu/>`_ has its own tools for working with
+genomic intervals under the "Operate on Genomic Intervals" section. A subset
+of complementary Bedtools utilities have also been made available on Galaxy in
+an effort to provide functionality that isn't available with the native Galaxy
+tools.
+
+ .. image:: images/galaxy-bedtools.png
+
+
+-------------------
+Pybedtools
+-------------------
+
+`Pybedtools <http://pypi.python.org/pypi/pybedtools>`_ is a really fantastic
+Python library that wraps (and extends upon) the bedtools utilities and exposes
+them for easy use and new tool development using Python. Pybedtools is actively
+maintained by Ryan Dale.
+
+
+-------------------
+MISO
+-------------------
+
+`MISO <http://genes.mit.edu/burgelab/miso/>`_ is "a probabilistic framework
+that quantitates the expression level of alternatively spliced genes from
+RNA-Seq data, and identifies differentially regulated isoforms or exons across
+samples." A subset of the functionality in MISO depends upon ``bedtools``. MISO
+is developed by Yarden Katz.
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
index f949104b7af8648d4b926058dd61ffbdc7db8ef1..c9df3e6ffea3ab461bc198c9c4f3fd2ebe20d291 100755
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -29,7 +29,8 @@ Table of contents
content/advanced-usage
content/tips-and-tricks
content/faq
-
+ content/related-tools
+
=================
Brief example
@@ -59,15 +60,11 @@ License
bedtools is freely available under a GNU Public License (Version 2).
=====================================
-Contributors.
+Acknowledgments
=====================================
-As open-source software, BEDTools greatly benefits from contributions made by other developers and
-users of the tools. We encourage and welcome suggestions, contributions and complaints. This is how
-software matures, improves and stays on top of the needs of its user community. The Google Code
-(GC) site maintains a list of individuals who have contributed either source code or useful ideas for
-improving the tools. In the near future, we hope to maintain a source repository on the GC site in
-order to facilitate further contributions. We are currently unable to do so because we use Git for
-version control, which is not yet supported by GC.
+
+To do.
+
=================
Mailing list