Downloadable scripts generated during MICROGEN project


Most of the scripts bellow need BioPerl installed.

NOTE: files are gzip compressed.

Readme
1. Perl. 

Preferably, ActivePerl from ActiveState. You should install it in
/usr/local/ActivePerl because thats where the programs assume it will be
found. If its installed, the following command 

which perl

should give you /usr/local/ActivePerl/bin/perl

If you choose to install it in another place, you have to change the 
path inside (the first line of the program) 

2. Bioperl

Go to www.bioperl.org and download latest bioperl and install it. Without
bioperl-based most programs will not work.


3. Extra suggested perl modules can be installed. All these can be obtained
from http:/search.cpan.org

	Error
	Graphics::ColorUtils
	Sort::Fields
	Statistics::Descriptive
	Text::ASCIITable
        Graphics::ColorUtils
	Regexp::Common
        Sort::Versions
        String::CRC
        File::Tail
        Bio::LITE::Taxonomy

        if perl is installed properly, you can use ppm to install several of these modules
        e.g.
             apt-get install Sort::Fields


4. Some programs might use internally programs from the EMBOSS package. These programs
should be available in the path

      for ubuntu users, install emboss like this..

          apt-get install emboss

5. R package  (get from CRAN http://www.r-project.org/ )
   you should install the following R packages..
	-     Hmisc
	-     vegan
	-     FactoMineR

6. Other useful programs 
    - trimAL       alignment trimming   (http://trimal.cgenomics.org )
    - trf          tandem repeat finder (http://tandem.bu.edu/trf/trf.html)
    - ssu-align    16s rRNA aligner (http://selab.janelia.org/software.html)
    - hmmer3       http://selab.janelia.org/software.html
    - mummer       http://mummer.sourceforge.net/


7. You can copy the programs to a folder and make them executables, e.g.
        chmod +x convertseq
   make sure to add the location of these programs to your $PATH variable.