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Post-processing of the files produced by tmVar is required before integrating it with other software components.
However, applying these methods implies an additional processing step for converting the files produced during research to formats suitable for archiving.
(i) A 'raw' zip archive contains the raw data files, i.e. the files produced by the microarray image analysis software, such as CEL files for Affymetrix GeneChips or GPR files from GenePix.
Moreover, XML is an easy to learn language and a well-designed schema (e.g. using descriptive and self-explanatory tags) allows an easy to understand reading of the files produced with it, also for people with limited computer skills (Barillot and Achard, 2000).
Because the number of reads alone is not a good measure of which filter might be superior in producing sequence data suitable for phylogenetics, the files produced from each filter were examined for average read length and number of contigs assembled (table 1).
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The Results page includes the files produces at several steps: the quality reports, the processed alignment in BAM format [ 31], reads and target coverage statics, the complete call results in vcf format [ 49] and the annotated table of variants.
For coordination and structural files, we read the last coordinate frame from the file produced by the 90 ns classical MD simulation as explained earlier [2].
The file produced was loaded into R and then filtered for the abundances at first and then for KEGG Orthology (KO) level of KEGG classification.
MarketBrief takes those hard-to-read SEC files and automatically converts them into news articles that are far more readable and easy to digest than the obtuse files produced by the SEC.
To make full use of the parallelized routines described in this paper, the serial PHYLIP suite is also recommended to be installed to be able to generate bootstrapped datasets and to analyze the output files produced by the parallel programs.
Digital-quality data were generated from the image files produced by the sequencer.
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