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+# chromeister
+An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.
+
+## Requirements
+
+GCC compiler (any version that is not completely outdated should do) and the R-base package (default R installation should do) with no extra packages.
+Simply download the .zip and unzip it, or clone the repository (currently the active branch is "histo-kmer-ultra" DO NOT USE ANY OTHER).
+Then issue the following commands:
+
+cd chromeister/src && make all
+
+You are ready to go!
+
+## Use
+
+There are several ways in which CHROMEISTER can be used. The simplest one is to run a 1-vs-1 comparison and then compute the score and the plot.
+To do so, use the binaries at the bin folder:
+
+CHROMEISTER -query seqX -db seqY -out dotplot.mat && Rscript compute_score.R dotplot.mat
+
+This will generate the comparison matrix, the plot of the comparison with the automatic scoring and the guides to be used in an exhaustive GECKO comparison.
+
+More to be added soon!
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