diff --git a/README.md b/README.md
index 3c4d704..9c02b3e 100644
--- a/README.md
+++ b/README.md
@@ -3,19 +3,18 @@
 Sequence element enrichment analysis. This document contains
 installation instuctions. Usage can be found on the [wiki](https://github.com/johnlees/seer/wiki/Usage), and more information in the [paper](http://www.nature.com/articles/ncomms12797).
 
-Installation
-==============
-###Use a pre-compiled release
+## Installation
+### Use a pre-compiled release
 
 Head to the [release](https://github.com/johnlees/seer/releases) page and download and unpack the tarball. If you have the dependencies installed use the dynamic version, otherwise use the static version (tested on Ubuntu only; static_all should work on other 64-bit Linux platforms).
 
-###Use on a virtual machine
+### Use on a virtual machine
 
 We have a virtual machine, containing SEER and other useful bioinformatics programs, which is available at
 ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
 and can be imported as an appliance in [VirtualBox](https://www.virtualbox.org/).
 
-###Compile source code
+### Compile source code
 
 First clone the repository
 
@@ -32,8 +31,7 @@ Currently tested on Linux only, installation should proceed as
 
 Full installation instructions are available <a href="#installation-on-ubuntubiolinux">below</a>
 
-Dependencies
---------------
+## Dependencies
 seer currently depends on
 
 - gzstream <http://www.cs.unc.edu/Research/compgeom/gzstream/>
@@ -49,7 +47,7 @@ You will also require
 
 You probably already have boost, HDF5 and dlib (as long as you did clone --recursive).
 
-###Installation on Ubuntu/biolinux
+### Installation on Ubuntu/biolinux
 
 Running the following commands will install seer
 
@@ -75,7 +73,7 @@ Running the following commands will install seer
     cd ..
     cd src && make CXX=/usr/bin/g++-4.9
 
-###General installation instructions
+### General installation instructions
 
 **gzstream**
 
@@ -142,6 +140,5 @@ do by running
     make CXX=g++-4.9
 
 
-Usage, interpretation of results, and troubleshooting
-=============
+## Usage, interpretation of results, and troubleshooting
 See the [wiki](https://github.com/johnlees/seer/wiki/Usage)
diff --git a/src/seerIO.cpp b/src/seerIO.cpp
index 7a5dac2..5f12edf 100644
--- a/src/seerIO.cpp
+++ b/src/seerIO.cpp
@@ -138,6 +138,7 @@ arma::mat readHDF5(const std::string& file_name)
 
 arma::mat readMDS(const std::string& file_name, const std::vector<Sample>& sample_names)
 {
+   std::map<std::string,unsigned int> mds_idx;
    arma::mat MDS = readHDF5(file_name);
 
    // Check that the sample names match up
@@ -147,31 +148,40 @@ arma::mat readMDS(const std::string& file_name, const std::vector<Sample>& sampl
       std::ifstream samples_in(sample_name_file.c_str());
       if (samples_in)
       {
-         arma::uvec keep_indices(sample_names.size());
-         unsigned int sample_row = 0;
+         arma::uvec keep_indices(MDS.n_rows);
          unsigned int file_row = 0;
 
+         // Read in sample file to get MDS row order
          while (samples_in)
          {
             std::string sample_name;
             samples_in >> sample_name;
-
-            // Must be ordered, and lines in sample_names be a subset of what
-            // is in the file. Otherwise a non-compatible mds will be returned
-            // which will throw
-            if (sample_name == sample_names.at(sample_row).iid())
+            if (samples_in)
             {
-               keep_indices(sample_row) = file_row;
-               if (++sample_row >= sample_names.size())
-               {
-                  break;
-               }
+               mds_idx[sample_name] = file_row;
             }
             ++file_row;
          }
 
+         // Get MDS rows (using sample file read above) in same sorted order as
+         // sample vector
+         unsigned int sample_row = 0;
+         for (auto it = sample_names.begin(); it != sample_names.end(); ++it)
+         {
+            auto find_it = mds_idx.find(it->iid());
+            if (find_it == mds_idx.end())
+            {
+               throw std::runtime_error("Could not find sample " + it->iid() + " in the pheno file");
+            }
+            else
+            {
+               keep_indices(sample_row) = find_it->second;
+            }
+            sample_row++;
+         }
+
          // Only keep the rows where the pheno file has data
-         if (sample_row == sample_names.size())
+         if (mds_idx.size() >= sample_names.size())
          {
             MDS = MDS.rows(keep_indices);
          }
diff --git a/src/seercommon.hpp b/src/seercommon.hpp
index 221bbc0..9a16465 100644
--- a/src/seercommon.hpp
+++ b/src/seercommon.hpp
@@ -41,7 +41,7 @@
 #include "covar.hpp"
 
 // Constants
-const std::string VERSION = "1.2alpha2";
+const std::string VERSION = "1.2alpha3";
 //    Default options
 const double maf_default = 0.01;
 const long int max_length_default = 100;