v0.1.3 Β· MIT Β· DOI 10.5281/zenodo.18472731 (all versions)

Bioinfoeasy

A Software Package for Simplifying Bioinformatics Analysis

A growing collection of small, self-contained tools for biological sequence analysis β€” codon usage bias, repeats and SSRs, selection pressure, format conversion and figures. Most of them are single Python scripts: you download them, you run them, your data stays on your machine.

↓ Download v0.1.3 View on GitHub Zenodo archive Try the online primer designer β†’

Hosted on this site Β· no GitHub account needed Β· MIT licensed

  • 40+tools & scripts
  • 5module groups
  • EN / CNbilingual interface
  • MITopen licence
  • 3.7+Python, 3.9+ advised

Why this package

Written for the analyses that actually eat your time

Every tool here started as something that needed doing repeatedly in a real project β€” often under reviewer pressure. They are deliberately small, readable and disposable: take the one you need, read its README, run it, move on.

Local first

Standalone scripts that run on your own machine. No upload, no account, no web service to go down mid-analysis.

Bilingual by construction

English (EN) and Chinese (CN) versions sit side by side, and the scripts behind them are identical.

Made for manuscripts

Figures go out as vector PDF/SVG and tables as CSV/XLSX, so results drop straight into a submission without re-drawing.

What you get

Features

πŸ’» CLI and GUI, your pick

Batch-friendly command-line scripts for pipelines, plus point-and-click GUIs for the same jobs when you only need to do it once.

🧬 Codon usage bias suite

ENC / GC3s, GC12–GC3 neutrality, Wright's neutral expectation test, RSCU aggregation with Kruskal–Wallis, and correspondence analysis with correlation tests.

πŸ” Repeats and SSRs

Direct and palindromic repeat statistics from Vmatch output, MISA parsing, and SSR classification into CDS / intron / intergenic space.

πŸ“Š Publication-ready figures

Codon usage, GC12–GC3, GC3–ENC, PR2 and COA plots, Pi sliding-window profiles, heatmaps and a phylogenetic time-scale generator.

πŸ”„ Format conversion

GenBank/GFF3 to mVISTA, GFF3 to BED, gene coordinates to 0-based BED, CodonW output to RSCU-Plot input, and general FASTA housekeeping.

πŸ”¬ Review-ready outputs

Several modules exist because a reviewer asked for exactly that table or figure β€” Ka/Ks filtering and imputation, regression tables, supplementary COA panels.

Repository map

Modules

Five top-level directories. Every module carries its own README, and most ship the smallest possible requirements.txt.

analyzer/

15 tools

The analytical core: codon usage bias statistics, chloroplast genome comparison and quadrant analysis, repeats, SSR classification, Ka/Ks handling.

codonw_analyzerGC_ENC_Analyzer ENC_GC3s_Analyzergc12_gc3_regression rscu_kruskal_wallisKaKs_Analyzer RepeatAnalyzerSSR_Region_Classifier misa_toolcp_genome_comparison

Plots/

12 tools

Everything that ends up as a figure, with versioned sub-directories so older plots stay reproducible.

draw_codon_usageGC12_GC3 GC3_ENCPR2_plot coa_plottercoa_simple_plotter Heatmapheatmap_gui pi_plottime_scale_generator

Seqinfo/

2 versions

Genome annotation analysis β€” summarise a GenBank record into the tables you actually need.

genome_annotation_analyzerv3.0.0

Seqtool/

8 tools

Day-to-day sequence plumbing: validate and fix FASTA, merge or rename records, convert between annotation formats, compare sample sets.

fasta_validatorfasta_joiner fasta_header_renamergff3_to_bed_converter gene_to_0genbank_to_mvista comparison

other_tools/

3 tools

Small utilities that refuse to fit anywhere else: batch renaming, CodonW-to-RSCU-Plot conversion, and a browser-based folder lister.

batch_renamer_toolcodonw2rscuplot file_lister

Conventions: language directories are EN / CN, versions are vMAJOR.MINOR.PATCH, directory names are snake_case, and superseded versions move to archive/ rather than being deleted.

Latest release Β· 17 Oct 2026

What's new in v0.1.3

This release centres on codon usage bias and repeat analysis, and most of it grew directly out of an ongoing peer review.

  • KaKs Analyzer β€” filters Ka/Ks results and imputes missing values, with .xlsx and .kaks auto-detected.
  • ENC-GC3s Analyzer β€” quantifies how many genes fall below, on, or above Wright's neutral expectation curve.
  • GC / ENC Analyzer β€” batch GC1/GC2/GC3/GC3s/GC12 and ENC (CodonW 1.4.4 compatible), with GC12–GC3 regression built in.
  • COA plotters β€” supplementary figures for CodonW correspondence analysis, with correlation statistics against GC3s / GC / GC12.
  • SSR Region Classifier & MISA toolkit β€” SSR classification into CDS / intron / IGS, plus publication-ready SSR figures.
  • Repeat Analyzer β€” direct and palindromic repeat statistics straight from Vmatch repfind output.
  • Also added β€” GC12–GC3 regression table, FASTA header renamer and CodonW2RSCUPlot.

Get the package

Download the latest release

The current release is mirrored on this server, so the download works even when GitHub is slow, blocked or unavailable. The mirror always follows the newest official release.

v0.1.3 Latest release

Full package Β· Python source Β· MIT licence

Released
17 Oct 2026
File
Bioinfoeasy_v0.1.3.zip
Size
2.8 MB
↓ Download ZIP GitHub release Zenodo record

Served straight from this site β€” no redirect to github.com, no login, no tracking. Unzip it and follow the Quick start below.

SHA-256 4ff2ab88c4e693bc15d1118c7c87ba36b7cdf5afab8a8535774e6dbd14a50f72

Earlier releases

Browse all releases on GitHub β†’

Version, size and checksum come from `downloads/releases.json`, regenerated from GitHub `releases/latest` whenever a new version is published.

Three commands

Quick start

Python 3.7 or newer (3.9+ recommended) and pip. Install the whole package, or just the dependencies of the single tool you need.

Install 
git clone https://github.com/Zmy0912/Bioinfoeasy.git
cd Bioinfoeasy
pip install -r requirements.txt

# or, for a single tool only
cd analyzer/KaKs_Analyzer
pip install -r requirements.txt
Run it 
# Summarise a genome annotation
cd Seqinfo/v3.0.0
python genome_annotation_analyzer.py chloroplast.gb

# Codon usage plot (English UI)
cd Plots/Codon_plot/draw_codon_usage/v0.1.1/EN
python draw_codon_usage_en.py -i input.fasta -o output.pdf

# Ka/Ks filtering and imputation (GUI)
cd analyzer/KaKs_Analyzer
python kaks_analyzer.py

# GC / ENC batch statistics (GUI)
cd analyzer/GC_ENC_Analyzer
python GC_ENC_Analyzer.py

Newer modules keep their Chinese documentation under a δΈ­ζ–‡/ sub-directory instead of CN/; both are supported and the scripts are identical.

Nothing to install

Also available in the browser

Primer Design PCR primer design driven by the real Primer3 (libprimer3), with hairpin and dimer sketches, a template position map and CSV/FASTA export. Falls back to a built-in engine when the server is unreachable.

If it helped

Citation

Cite Bioinfoeasy if it helped your work. Choose a DOI, then copy a citation in the format your manuscript or reference manager needs β€” or download the file directly.

  • Cite all versions β€” concept DOI Recommended 10.5281/zenodo.18472731 One DOI for every release. It always resolves to the latest version, so readers get whatever is current.
  • Cite one version β€” version DOI 10.5281/zenodo.23430885 v0.1.3 (released 2026-10-17). Pin this only when you need to reference the exact code you ran; older releases have their own DOIs on the Zenodo record.

Ready-to-use citations

Every field is filled in for you. Pick a style, copy the text, or download a file for Zotero, EndNote, JabRef or your manuscript.

Cite with
BibTeX

Same metadata as the repository's `CITATION.cff`. Switching the DOI above updates `doi`, `url` and `version` in every format.