fix a move

3 files changed, 79 insertions, 79 deletions

diff --git a/doc/README.markdown b/doc/README.markdown
index 82004aa..1aad66b 100644
--- a/doc/README.markdown
+++ b/doc/README.markdown
@@ -1,47 +1,32 @@
-# How Can I Install The Quikr Utility? #
-To use Quikr there are several prerequisites. 
-
-## Requirements ##
-+ Mac OS X 10.6.8 or GNU/Linux
-+ 4Gb of RAM minimum. Absolutely neccessary.
-+ gcc that supports OpenMP
-
-### Python Requirements ###
-+ Python 2.7
-+ Scipy 
-+ Numpy
-+ BioPython
-
-### Mac Requirements ###
-+ Mac OS X 10.6.8 (what we have tested)
-+ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation)
-+ OCaml compiler mlton
-+ OpenMP libraries (libgomp, usually comes with gcc)
-
-### Linux Requirements ###
-+ GCC 4.7 or newer
-+ OCaml compiler mlton
-+ OpenMP libraries (libgomp, usually comes with gcc)
-
-We also have a Quikr implementation in Matlab so that you can easily integrate
-Quikr into your custom programs and scripts.
-
-### Installation ###
-Our Quikr code is available on our sourceforge download page:
-
-[http://sourceforge.net/projects/quikr/](sourceforge project page)
-
-Our development GIT repository is available here:
-
-[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/)
-
-To install quikr, download our project and in the folder run:
-
-    make
-    sudo make install
-
-This will install the quikr, quikr\_train and multifasta\_to\_otu utilities.
-To install the python scripts and module systemwide, run
-
-    make python
-    sudo make install_python
+# Quikr #
+This is the homepage for quikr.
+
+## What is Quikr ##
+Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that
+utilizes sparsity promoting ideas from the field of compressed sensing to
+reconstruct the composition of a bacterial community (when the input data is
+454-like pyrosequencing data). This extremely fast method comes with a default
+training database but can be custom trained. Typically reconstruction is
+accurate down to the genus level.
+
+
+## How Do I Install Quikr ##
+Please read the directions on the [installation page](install.markdown).
+
+## How Do I use Quikr ## 
+We have several ways to use quikr. Quikr is first and formost a command
+line utility, but we also provide python and matlab scripts.
+
++ [Command Line Utilities](cli.markdown)
++ [Matlab documentation](matlab.markdown)
++ [Python documentation](python.markdown)
+
+## Contact ##                                   
+For issues with the quikr software, contact gailro@gmail.com
+
+## Contributors ##
++ David Koslicki
++ Simon Foucart
++ Gail Rosen
++ Calvin Morrison
++ Jean-Luc Bouchot
diff --git a/doc/index.markdown b/doc/index.markdown
deleted file mode 100644
index 1aad66b..0000000
--- a/doc/index.markdown
+++ /dev/null
@@ -1,32 +0,0 @@
-# Quikr #
-This is the homepage for quikr.
-
-## What is Quikr ##
-Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that
-utilizes sparsity promoting ideas from the field of compressed sensing to
-reconstruct the composition of a bacterial community (when the input data is
-454-like pyrosequencing data). This extremely fast method comes with a default
-training database but can be custom trained. Typically reconstruction is
-accurate down to the genus level.
-
-
-## How Do I Install Quikr ##
-Please read the directions on the [installation page](install.markdown).
-
-## How Do I use Quikr ## 
-We have several ways to use quikr. Quikr is first and formost a command
-line utility, but we also provide python and matlab scripts.
-
-+ [Command Line Utilities](cli.markdown)
-+ [Matlab documentation](matlab.markdown)
-+ [Python documentation](python.markdown)
-
-## Contact ##                                   
-For issues with the quikr software, contact gailro@gmail.com
-
-## Contributors ##
-+ David Koslicki
-+ Simon Foucart
-+ Gail Rosen
-+ Calvin Morrison
-+ Jean-Luc Bouchot
diff --git a/doc/install.markdown b/doc/install.markdown
new file mode 100644
index 0000000..82004aa
--- /dev/null
+++ b/doc/install.markdown
@@ -0,0 +1,47 @@
+# How Can I Install The Quikr Utility? #
+To use Quikr there are several prerequisites. 
+
+## Requirements ##
++ Mac OS X 10.6.8 or GNU/Linux
++ 4Gb of RAM minimum. Absolutely neccessary.
++ gcc that supports OpenMP
+
+### Python Requirements ###
++ Python 2.7
++ Scipy 
++ Numpy
++ BioPython
+
+### Mac Requirements ###
++ Mac OS X 10.6.8 (what we have tested)
++ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation)
++ OCaml compiler mlton
++ OpenMP libraries (libgomp, usually comes with gcc)
+
+### Linux Requirements ###
++ GCC 4.7 or newer
++ OCaml compiler mlton
++ OpenMP libraries (libgomp, usually comes with gcc)
+
+We also have a Quikr implementation in Matlab so that you can easily integrate
+Quikr into your custom programs and scripts.
+
+### Installation ###
+Our Quikr code is available on our sourceforge download page:
+
+[http://sourceforge.net/projects/quikr/](sourceforge project page)
+
+Our development GIT repository is available here:
+
+[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/)
+
+To install quikr, download our project and in the folder run:
+
+    make
+    sudo make install
+
+This will install the quikr, quikr\_train and multifasta\_to\_otu utilities.
+To install the python scripts and module systemwide, run
+
+    make python
+    sudo make install_python