Software
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All free computer programs on this page can only run with the R platform already installed on your system. The programs work under windows, linux, and macOS. Please visit 
CRAN to get more information about how to install R.
MultiCoLA
Description: Multivariate Cutoff Level Analysis (MultiCoLA) - A strategy to systematically assess the impact of rarity definition on large community datasets and on their further ecological interpretations.
The zipped folder includes a manual, examples and the R scripts.
Last updated 22 July 2010
Automatic binner
Description: The script performs an automatic binning of fragments into OTUs from GeneMapper output text files (samples, peak sizes, peak areas) and identifies the best combination of the window size (WS) and of the shift (Sh) value. This enables an optimal determination of the best binning strategy for a dataset without a priori knowing the ideal WS value. A compromise between high resolution (low WS) and high similarity among samples (high WS) must be found based on the output of the script. Note that the script may take a long time to run, especially if the number of samples being compared is high.
The zipped folder includes a manual, examples and the R script.
Last updated: 20 October 2008
Interactive binner
Description: A shifting window size binning strategy is implemented as it offers the possibility to optimally aligned electrophoretic profiles and to deal with different window starting positions. The binning frame that offers the highest similarity among samples is identified out of all binning frames starting at a given position. The distance between two consecutive binning frames is defined as the Shift (Sh) value. The current implementation of the window shifting algorithm enables a user-defined choice of WS and Sh values to calculate the best binning frame for a given data set. The script then reports the best frame among all calculated as the one that maximizes sample similarities.
The zipped folder includes a manual, examples and the R script.
Last updated: 22 April 2009
qfingerprinting
Description: The script calculates the abundances of identified operational taxonomic units (OTUs) when using the qfingerprinting strategy. The input data consist of a binned table of rows of replicated dilutions by OTUs. The abundance of each OTU is then estimated according to the consensus and continuity rules.
The zipped folder includes a manual, examples and the R script.
Last updated: 20 October 2008