Update README.md

README.md

@@ -12,18 +12,18 @@ Compute local minima and energy barriers of a landscape
 
 ## INSTALLATION
 
-Typically, barriers in installed like this:
+Typically, `barriers` in installed like this:
 
 ```
 ./configure
 ./make
 ./make install
 ```
 
-The barriers program uses a large static array for the hash table at the
+The `barriers` program uses a large static array for the hash table at the
 heart of the method. The size of this hash and therefore the maximum size
 of the landscape you can analyse is set at compile time using the
-`--with-hash-bits` option of the configure script, e.g.:
+`--with-hash-bits` option of the `./configure` script, e.g.:
 
 ```
 ./configure --with-hash-bits=27
@@ -32,20 +32,20 @@ of the landscape you can analyse is set at compile time using the
 will create a hash of 2^27 entries.
 
 If you you need a hash size >2^27 you may have to set the `-mcmodel=medium`
-or `-mcmodel=large` option in gcc, e.g.:
+or `-mcmodel=large` option in `gcc`, e.g.:
 
 ```
 ./configure --with-hash-bits=29 CFLAGS='-mcmodel=medium'
 ```
 
-You can use the script 'scripts/get_hashbits.pl' to optimize the hashsize
+You can use the script `perl/get_hashbits.pl` to optimize the hashsize
 given your RAM size and sequence length.
 
 ----
 
 ## IMPORTANT NOTES
 
-With version 1.7.0, the default move set (`-M`) for RNA graphs changed from
+With version 1.7.0, the default move set (`-M`) for `RNA` graphs changed from
 Shift moves to just insertion/removal of single base pairs! To reproduce
 results obtained with barriers prior to 1.7.0, you need to explicitly
 activate the Shift move option, e.g.:
@@ -62,13 +62,13 @@ For an explanation of the algorithm, please see
 
 Ch. Flamm, I.L. Hofacker, P.F. Stadler, M.T. Wolfinger.
 Barrier trees of degenerate landscapes. 
-Z. Phys. Chem., 216:155--173, 2002. (doi:10.1524/zpch.2002.216.2.155)
+Z. Phys. Chem., 216:155--173, 2002. [doi: 10.1524/zpch.2002.216.2.155](https://doi.org/10.1524/zpch.2002.216.2.155)
 
 Ligand support has been added with version 1.7.0, see
 
 M.T. Wolfinger, Ch. Flamm, I.L. Hofacker
 Efficient computation of cotranscriptional RNA-ligand interaction dynamics
-Methods, 2018 (doi: 10.1016/j.ymeth.2018.04.036)
+Methods, 2018 [doi: 10.1016/j.ymeth.2018.04.036](https://doi.org/10.1016/j.ymeth.2018.04.036)
 
 ----
 
@@ -77,7 +77,7 @@ Methods, 2018 (doi: 10.1016/j.ymeth.2018.04.036)
 Copyright (C) 2001 Ivo Hofacker, Christoph Flamm, Peter Stadler, Michael
 T. Wolfinger
 
-barriers is free software; you can redistribute it and/or modify it under
+`barriers` is free software; you can redistribute it and/or modify it under
 the terms of the GNU General Public License as published by the Free
 Software Foundation; either version 2 of the License, or (at your option)
 any later version.