BioAider v1.727

Compared to BioAider v1.627

• Added the Sequence Editor, used for browsing/editing sequences, and generating sequence alignment figure.

• Provided the graphical interfaces for HMMER tools (including hmmbuild, hmmsacn and hmmsearch), to facilitate parameter setting and usage. They are loaded as plugins at the user's choice in BioAider. Thanks to development teams of HMMER software.

• Updated the function Viral *.gb file parser, since NCBI replaces label country with geo_loc_name.

• Added a right-click menu to the file system on the main interface.

BioAider v1.627

Compared to BioAider v1.532-beta

Optimized the calculation function of Mutation Analysis

• Multi-process-based parallelization was used in calculations, and the calculation logic has been optimized. Now, the run times are drastically reduced, and what used to take hours can now be done in minutes. We tested about 87,000 ORF1ab sequences from SARS-CoV-2, if 4 cores are used in the desktop computer (Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz ), and the analysis is completed in about 3 minutes.

• Optimize memory usage. Sequences in the alignment can be iteratively read and loaded into memory, which allows large amounts of sequences to be computed at lower memory. This is optional using the parameters Max.num.seqs in interative , default value: 20000 sequences.

Updated the function of Date converted to Decimal

• Batch processing of multiple formats is supported.

# Eaxmple 1
# mix of YYYY, YYYY.MM and YYYY.MM.DD
2013
2014.05
2015.10.01

# Eaxmple 2
# mix of YYYY, YYYY_MM and YYYY_MM_DD
2013
2014_05
2015_10_01

# Eaxmple 3
# mix of YYYY, YYYY/MM and YYYY/MM/DD
2013
2014/05
2015/10/01

# Eaxmple 4
# mix of YYYY, YYYY-MM and YYYY-MM-DD
2013
2014-05
2015-10-01

# Eaxmple 5
# mix of separators including '-', '/', '-' and '_'
2022.11-11
2022/11.11
2022_11-11

Others

• More tips of usage were added in software interface, Chinese language included.（在软件界面增加更多的使用提示，包括中文的）

• Optimization of parallel computations in K-mer Matrix of Sequences and Viral *.gb file parser.

BioAider V1.532-beta

Compared to BioAider V1.527

Add new functions

• Add an extra output file in the Combination nt and aa (nt/aa) function of Sequence Identity Matrix, according to the user's proposed needs. The extra output data was used to draw heatmaps, below the diagonal is nucleotide identity and above diagonal is amino acid identity.

• In the codon-based function, allow both base T and base U to exist in the input sequence-file, BioAider replaces all base U with base T before the calculation in these sections below,

  • The codon-alignment method based on MAFFT, Muscle and Clustal-Omega plugins.

  • the codon-based options in Mutation Analysis, Sequence Identity Matrix and Sequence Vary(nt → aa translation).

  • Tip: still, we want you to import consistent sequences correctly.

• Change the import method of MAFFT, Muscle, Clustal-Omega and FastTree plugins, the new version using the Manage plugins menu instead of requiring external_program.zip.

Fix bugs

• In the previous Ambiguous Base Edition, if there is not stop-codon at the end of the sequence, the last three bases will be deleted by mistake. This bug was fixed by the original contributors (Xiyue Wang).

BioAider V1.527

Add new functions

• Provides tools for hierarchical clustering based on k-mer features of nucleotide sequence.

• Added options for nucleotide, codon and amino acid in the Linked mode of Mutation Analysis.

• For codon data, add the output result in Mutation Analysis that can be used to draw mutant lollipops.

• Support multiple opening of the same pop-up window to run multiple data at the same time.

• Provides an efficient electronic-lab-notebook to support recording experiments and managing them.

• Increase update detection of software version, including manual and automatic one.

• Support changing font and font size of software.

• Add codon-extraction function in Sequence Vary, including two modes, (1, 2 , 3) and (1 + 2, 3).

• Support adding and deleting shortcuts, quickly access other software while using BioAider.

• Provide graphical interfaces for some classic command-line programs

  • Provide the graphical interfaces for IQ-Tree, MrBayes and ModelFinder softwares, to facilitate parameter setting and usage. These tools are loaded as plugins at the user's choice in BioAider. Thanks to development teams of these classic softwares.

  • Added conversion tool of model parameter, and easily prepare model-files for IQ-Tree and MrBayes When the sequence data is partitioned.

  • Provide a graphical interface for Blast, to facilitate parameter setting and usage. The Blast program is loaded as plugin at the user's choice in BioAider. Greatly simplify library construction and sequence alignment, and provide convenient management of multiple databases. Thanks to development team of Blast software.

Fix bugs in version 1.423

• The function of Repeat Fragment Search cannot work in BioAider V1.423.
• The Remove High-Similar sequences cannot work in BioAider V1.423.
• The file directory of the main interface cannot be automatically updated in BioAider V1.423.
• Some bugs on sorftware interface. Optimize interactive operation and beautify the interface.

BioAider V1.423

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.

BioAider V1.334

• Add the following functions:

  • Viral *.gb file parser: Extract the information from virus *.gb file, such as host, collection date and country, reference article, etc. What's more, BioAider can be extracted and stored according to species relationship.
  • Ambiguous Base Edition: Processing ambiguous bases and premature stop codons (preparing sequences for PAML analysis). This feature was contributed by Xiyue Wang. In addition, the authors suggest: (i) the content of ambiguous bases in a single sequence should not be greater than 2%; (ii) it is not suitable to correct the ambiguity base sites in those sequences with long genetic distances.
  • Delete Low-Similar Sequence: Removing sequences with similarity below the threshold.
  • Date converted to Decimal: Convert date to decimal.
  • Sequence Batch Download (NCBI): NCBI sequence batch search.
  • File Merge: Simple function of combining multiple files into one file.
  • Increased the output linked mutation sites and re-beautified the mapping in Mutation Analysis function.
  • Provide graphical interface for FastTree software, to facilitate parameter setting and usage. Thanks to the FastTree development team. The copy of FastTree software is in https://github.com/ZhijianZhou01/plugins. If you need it, please unzip external_program.zip and put the directory external_program in the root directory of the BioAider.

• Fix bugs

  • Fixed the bug that the number of stop codons sometime cannot be counted in the summary file in Mutation Analysis function.

• Please pay special attention:
  On April 24, 2021 (International Veterinary Day), we uploaded the BioAider distribution for MacOS system for the first time, and fixed some bugs in the last uploaded windows and linux version (but keep the version number 1.334 unchanged).

BioAider V1.314

• Add the feature of looking for repetitive fragments.
• Add the feature of locating the protein to the nucleotide sequence.

BioAider V1.03

• Rewrite and beautify the interface of program, add more prompts for controls.
• Add a Linux dsitribution (GUI) for Ubuntu (16.04 and more) users.
• Added multiple sets of codon table in multiple-sequence alignment and in features of Mutation Analysis.
• Add variation analysis of non-coding gene and amino acid sequence in features of Mutation Analysis.
• Increased the pop-up window of program bug and toolbar for some common features.
• Add some new other features and fixed some bugs.
• Provide graphical interfaces for three popular multiple-sequence alignment tools (MAFFT, Muscle, Clustal-Omega), to facilitate parameter setting and usage. What's more, provide translation-alignment for codon gene. The copy of these tools is in https://github.com/ZhijianZhou01/plugins. Thanks to the developers of these programs. If you need them, please unzip external_program.zip and put the directory external_program in the root directory of the BioAider.

BioAider V1.0

• The first version of BioAider V1.x.