Technical Details ˇ
Source Code
Technical FAQ
Citation & Credit ˇ
How to Cite
Acknowledgements

 

You will need to install both Chromaseq, as well as Phred, Phrap, and Phd2Fasta.

Installing Chromaseq

To install Chromaseq, go to the download page and follow the instructions.

Acquiring Phred and Phrap

You can either acquire Phred and Phrap as source code (see How to Get Phred/Phrap/Consed), which most people at academic institutions can obtain free, or you can purchase precompiled versions from CodonCode Corporation. Note that Chromaseq does not require Consed, and so you will not need to obtain Consed for use with Chromaseq.

Please note that for most newer operating systems (ones that are 64-bit operating systems, e.g., MacOS X 10.6 or later on a Mac purchased in the last few years) older versions of Phrap will fail to run properly. To use Phrap (and thus Chromaseq) on these newer operating systems, you need to get the newest version of Phrap (which, at the time of writing, is 1.090518).

Compiling Phred, Phd2Fasta, and Phrap

If you are not familiar with compiling source code into executable programs, you may wish to ask for help from a local expert. (Not us.) Basically, you are taking the source code, present as text written in the computer language C, and asking a compiler to convert that text into machine code that your computer can understand. To do this, you will need access to a compiler. Here are some basic instructions, but they cannot be guaranteed to work on all computers.

Preparing the source code

You will receive the source code as archives, in three pieces, which might have names like this:

Unzip/untar these archives, so that you now have three directories on disk, which might have names like this:

Each of these directories contain the source code for different programs, and you will need to compile each one.

Creating the program directory

You will also need to create a directory to house the finished programs. We will imagine that you have created it and that it is called "phredphrap".

Compiling the programs

Sorry, but we cannot provide help to you in your attempt to compile these programs. For help you will need to be in touch with your local computer guru. If you find any error in the instructions below, please send us an email (), and we can update this page.

To compile the programs, following these instructions:

MacOS X, Linux

Windows

Making sure you have the approriate shell

Ubuntu

On some versions of Ubuntu, there will be no c-shell installed by default. As Chromaseq will need to invoke a c-shell for giving commands to phred and phrap, it must be installed. To see if you have a c-shell installed in the necessary directory, open a Terminal window and type:

   locate bin/csh

The terminal should return, at least:

   /bin/csh

if the shell is installed. If it is not installed (/bin/csh wasn't listed after the locate command), you can install it by entering, in the Terminal:

   sudo apt-get update
   sudo apt get install csh

This will install Ubuntu's c-shell; you can confirm proper installation by using the locate command as above.

Other Linux variants

For other Linux variants, you should also make sure you have a c-shell installed. Follow the instructions for Ubuntu, above, but apparently (please give us feedback if this is not the case) the command to install the shell is not the two "sudo apt-get" commands mentioned above but instead

   sudo yum install tcsh

 

Preparing the Phred Parameter File

In order for Phred to function properly, you will also need to edit the Phred parameter file. An initial version of the file should be present with the original distribution of Phred, and is called phredpar.dat. You will quite probably need to edit this file; you should probably make a copy of it and put it in an accessible spot, perhaps in the phredPhrap program directory. This file needs to contain, among other things, information about the dye chemistry and so on used by your particular automated DNA sequencer.

If you don't modify this file, the Mesquite/Phred/Phrap system may not function correctly, and it make not give obvious warning messages. If you look into the text written to your shell or Terminal program as Phred is running, you will see warnings of the following sort:

./DNA0446.b.wg578F.ab1: unable to match primer ID string: skipping chromatogram
unknown chemistry (DT3730POP7{BDv3}.mob) in chromat ./DNA0446.b.wg578F.ab1
add a line of the form
   "DT3730POP7{BDv3}.mob" <chemistry> <dye type> <machine type>
to the file /phredPhrap/phredpar.dat

If you see these warnings, it means that the appropriate entry for your sequencing machine or chemistry is not included in the default phredpar.dat file, and you will need to enter it. If you open up phredpar.dat file in a simple text editor, you will see lines of the following sort:

"DT3100POP6{BDv3}v1.mob" terminator big-dye ABI_3100

and you will need to add addition lines to the file of this form that contains the information relevant to your sequenching machine. For example, over time we've had to add the following lines:

"DT3730POP7{BDv3}.mob" terminator big-dye ABI_373_377
"DT3700POP5{BDv3}v1.mob" terminator big-dye ABI_3700
"DT377{BDv3}v2.mob" terminator big-dye ABI_373_377
"DT377{BDv3}v1.mob" terminator big-dye ABI_373_377
"KB_3100_POP4_BDTv3.mob" terminator big-dye ABI_3100
"KB_3730_POP7_BDTv3.mob" terminator big-dye ABI_373_377
"DT3700POP6{BDv3}v1.mob" terminator big-dye ABI_3700
"DT3730POP7{BDv3}.mob" terminator big-dye ABI_373_377

Note that the warning from Phred states what the first part of the line should contain. The phred.doc file contains more details.

Once you have your programs in a directory, and your phredpar.dat file modified, you should be able to use Chromaseq.