GenBank2Treedyn etract annotations from GenBank files for:
More convenient alignments and phylogeny (replace def line of fasta file by GI number)
Extremely powerfull annotations of phylogenetic trees with TreeDyn.
Glob-mapper is required to plot Event-mapper and Peak-mapper data and to extract hot spots (gene clusters) from the Event maps. Glob-mapper will search for the input data in a directory with pre-computed *.dat and *.sgn files generated by Event- or Peak-mapper, Glob-mapper also requires an identification file, containing genes ID and other information (a sample file is provided). This information will be displayed for the extracted genes. The ID file must contain at least three columns of data: 1 – unique profile identifier, 2 – gene identifier or CG number, this information will be extracted, 3 (must be the last column) – user-defined score value, this value is used to display a subset of the entire data on Event maps. Using this value user can, for instance, display all genes of a given pathway, which may serve as a marker in the analysis of the global gene expression.
EPIG (Extracting Patterns and Identifying co-expressed Genes) is a method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes. Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratios, EPIG extracts a set of patterns representing co-expressed genes without a pre-defined seeding of the patterns.
FCSExtract utility is to extract Flow Cytometry Standard (FCS) data from a binary FCS file and convert it to an ASCII text format, which can be read by a variety of software analysis packages.
g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier.