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BioAider V1.423
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@ZhijianZhou01 ZhijianZhou01 released this 21 Mar 14:01
· 275 commits to master since this release
1.423
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Learn about vigilant mode.

Fix bugs

  • (Important) the output result of "Codon method" in Mutations Analysis.

    • Resolved the bug that could not correctly plot the frequency distribution of synonymous and non-synonymous substitution sites using "base" as the statistical unit (the result of _substitution frequency distribution.pdf and _single syn or non-syn substitution nt sites.csv and *_Frequency group of sys and non-sys substitution.txt) when there are a large number of different kinds of mutations at the same codon site (e.g. sequences are from different genera or species, or large number of dinucleotide and trinucleotide substitution sites). Note that even if this bug is resolved, it is not recommended to apply it to the sequence sets with a large variety of variants at the same codon site, because it maybe no real value to count the number of nucleotides sites based on mutation frequency.
      Tip: Statistical results (such as *_all site.csv and *_mutation site.csv) using codons as units are correct for any sequences in the previous versions.

    • Resolved the bug that incorrect count of nt in Others information part in the end of _mutation site summary.txt when there are a large number of dinucleotide and trinucleotide substitution sites in sequence sets.
      Tip: Except for the Others information part, everything else in _mutation site summary.txt is correct in the previous versions.

  • Solved the problem that Delete Lower similar sequences cannot run in BioAider v1.334.

  • The problem that the input file or directory cannot contain .

Add new functions

  • (New and important) Optimized algorithm to greatly speed up BioAider, and quickly perform mutation analysis on hundreds of thousands of pieces of data (2022/03/24).

  • Codon method of Mutation Analysis add the option to delete nt sites with both synonymous and nonsynonymous substitution freely when drawing the graph of frequency distribution of synonymous and non-synonymous substitution sites.pdf.

  • (New and important) Function for drawing a lollipop map of gene (or genome) mutation sites.

  • Function to draw scatter, boxplots, violin diagram for data based on seaborn package (GUI interface).

  • Function to switch various themes freely.

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