ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constrains
Open the Command Prompt. In the same directory as the file ProtASR2.2.zip, type:
unzip ProtASR2.2.zip
You should now see a folder called ProtASR2.2. Note that this zip file was made on a mac, so in windows or linux you might see some strange files, that start with "." or "-". These are macintosh hidden files, which can be safely removed without affecting the software.
Two versions are available for ProtASR2.2.: Version A (folder ProtASR_vsA) and version B (folder ProtASR_vsB)
Version A allows inference from an alignment with length equal to the length of the PDB file.
Version B allows inference from an alignment with length different to the length of the PDB file, but a sequence of the alignment is equal to the sequence of the PDB file (gaps can be included).
A makefile is provided for the gcc compiler, but if you have cc instead, just change gcc for cc in the makefile. The default optimization level is set to -O3. To compile in macintosh with an intel processor, and probably in othe machines, you can enable the option -fast instead.
The compilation will generate an executable of the programs Prot_Evol and an adapted version of PAML, both included in the folder src.
To compile the program move into the folder src folder and type:
make all
to compile the executable in the current folder, or
make clean
to clean and remove executable files (saving HD space),
The program runs in a command-line window.
should open the Command Prompt. To run the program move to the folder where the executable is located and type:
perl ProtASR_main.pl Settings.txt
Parameters should be specified in a text file (e.g., "Settings.txt") that should be located in the same directory as the executable. Note that other files should also be placed in the directory (e.g., alignment file in nexus format with a tree in Newick format and a PDB file), see examples.
We recommend to read the documentation placed in the folder "doc" before using ProtASR.
This program 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. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
Miguel Arenas - miguelmmmab@gmail.com / marenas@uvigo.es
Ugo Bastolla - ubastolla@cbm.csic.es