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A base-10 log scale is used for the Y-axis of the bottom left graph, and the Y-axis ranges from 0.1 to 1000. The top right graph uses a log-10 scale for just the X-axis, and the bottom right graph uses a log-10 scale for both the X axis and the Y-axis. Presentation of data on a logarithmic scale can be helpful when the data:
A log–log plot of y = x (blue), y = x 2 (green), and y = x 3 (red). Note the logarithmic scale markings on each of the axes, and that the log x and log y axes (where the logarithms are 0) are where x and y themselves are 1. Comparison of linear, concave, and convex functions when plotted using a linear scale (left) or a log scale (right).
In 2007, a similar Python project, namely PyCogent, was established. [9] The initial scope of Biopython involved accessing, indexing and processing biological sequence files. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology (see Key features and examples).
A log-log chart spanning more than one order of magnitude along both axes: Semi-log or log-log (non-linear) charts x position; y position; symbol/glyph; color; connections; Represents data as lines or series of points spanning large ranges on one or both axes; One or both axes are represented using a non-linear logarithmic scale; Streamgraph
Software to build and analyze ensembles of genome-scale metabolic network reconstructions [61] Systems biology: Gregory L. Medlock, Thomas J. Moutinho, Jason A. Papin: 2001 Molecular Evolutionary Genetics Analysis (MEGA) Provides multiple algorithms to construct phylogenetic trees, including UPGMA, Maximum Likelihood, Maximum Parsimony, etc
Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
The linear–log type of a semi-log graph, defined by a logarithmic scale on the x axis, and a linear scale on the y axis. Plotted lines are: y = 10 x (red), y = x (green), y = log(x) (blue). In science and engineering, a semi-log plot/graph or semi-logarithmic plot/graph has one axis on a logarithmic scale, the other on a linear scale.
Log-log transformation places numbers into a geometric domain so that proportional deviations are represented consistently, independent of the scale and units of measurement. In biology, this is appropriate because many biological phenomena (e.g., growth, reproduction, metabolism, sensation) are fundamentally multiplicative. [22]