Table of tools and example files


The MacPerl version of the Perl programs can be downloaded as hqx-encoded archive. It includes all necessary libraries. MacPerl can be optained via anonymous ftp.

The UNIX/Linux versions are listed in the table below. All files - except logo5mC - are in text-format. Use the left mouse button under Netscape and compatibles and the right mouse button under InternetExplorer to download the files.

A SVG generating version of the programs can be downloaded as tgz-encoded archive (courtesy of Anup Madan) methools_SVG_Archive.tgz. Needs GD::SVG.

Tools

convert_bisulfite

converts bisulfite generated sequences in 'filename' into seq1- and seq2-format

PERL 5

download

EvalLog

determines the errors of the PCR and/or the sequencing reaction

PERL 5

download

InfoScan

searches for conserved methylation patterns

PERL 5

download

logo5mC2

generates graphical representation of methylated consensus sequences as LOGO (needs to be decompressed before installation)

c++

download

Plot_CpGs_to_ps

generates a graphical representation of methylation in CpG as postscript file (b/w version)

PERL 5

download

Plot_CpGs_to_png

generates a graphical representation of methylation in CpG as PNG file (color version)

PERL 5

download

Plot_CpNpGs_to_png

generates a graphical display of methylation in CpG and certain CpN as PNG file (color version)

PERL 5

download

Plot_CpNpGs_to_png

generates a graphical display of methylation in CpG and certain CpN as png file (color version)

PERL 5

download

Plot_5mCpG_density_to_png

plots the 5mCpG density distribution in individual sequences as png-image

PERL 5

download

Plot_5mC_density_to_png

plots the 5mC density distribution in individual sequences as png-image

PERL 5

download

Data

methylmx

matrix-file for ClustalW. The use of this matrix usually minimizes additional manual editing.

matrix

download

Examples

autometh.sh

tc-shell script that runs all programs consecutively. Usage: autometh.sh filename

tc-shell

download

example A

example data set A (input file for convert_bisulfite.pl)

FASTA

download

example B

example data set B

FASTA

download

infocont.tab

example infocont.tab (table of frequencies and information content)

table

download

logo.ps

example logo-output

postscript

download