FaBox FAQ
 

How to cite FaBox in a paper

Villesen, P (2007), FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968.
doi:10.1111/j.1471-8286.2007.01821.x

or

Villesen, P (2007), FaBox: an online fasta sequence toolbox, https://birc.au.dk/~palle/php/fabox/

Contact information

Palle Villesen Fredsted
Bioinformatics Research Centre, Aarhus University
Build. 1110, CF Moellers Alle 8
DK - 8000 Aarhus C
Denmark 		mobile: +45 2447 1214
email: palle[at]birc.au.dk

FaBox runs out of memory / large sequence sets!

FaBox is written in PHP and ONLY RUNS ON A WEBSERVER!!! I do NOT have the possibility to increase the memory allowed, so the only workaround is to:

1. download FaBox

2. Install it to your OWN webserver

3. Configure your OWN webserver allowing a lot of memory usage

But then the main idea is lost, so I suggest you find some other software that will do it for you - or team up with some bioinformaticians (collaborations are welcome, just email me).

Download FaBoX and run it on your own webserver

Direct download of FaBox: Download zip file
Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER!!!

Installation instructions

Unzip the files to a directory on your webbrowser.
Then you may edit the file "config.inc.php" in order to enable:
  • Logging by google analytics
  • Logo image on/off

About FaBox

  • FaBox is a collection of online tools that are useful for population biologists who are working with sequence datasets
  • The basic concept is simple: one service performs one task
  • Sequences need to be in fasta format

The toolbox is developed to help the handling of DNA and protein sequences and is usefull when you either

  1. Doesn't want to install software
  2. Want to do something specific with your dataset, and can't find it in your installed software (in this case you may have to write me an email and request a particular service)

Typically I have often wanted to be able to combine the description of my data (often in excel spreadsheets) with the actual data (often DNA sequences). Hence the first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison.

Also, producing correct input files for a range of programs seems to be problematic for the average user. The advantage of a converter is that it is guaranteed to work. Hence, I have included some converters in some of the services as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you'll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs.

This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use.

For many bioinformaticians these tools are trivial and can be re-written in seconds. For the general user, they are quite likely to be useful.

Please see individual help files for each service.