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The phase machine program allows supervised classification of DNA sequence data from different populations using haplotype sequences generated by the PHASE program.
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...trimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Among trimAl’s additional features, trimAl allows getting the complementary alignment (columns that were trimmed), to compute statistics from the alignment, to select the output file format , to get a summary of trimAl’s trimming in HTML and SVG formats, and many other options.
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