SimPlot-CL v1.0.4

Updated distance models, gap handling, and more!

What's Changed

New features

• Multiple distance models: Five pairwise distance models are now available via --distance-model (-dm): p-distance (pdist, default), Jukes-Cantor 69 (jc69), Kimura 1980 (k80), Hasegawa-Kishino-Yano (hky), and Tamura-Nei 93 (tn93).
• Gap handling: The --gaps parameter has been removed; all models now consistently strip any position where either sequence contains a gap or ambiguous character. A new --max-gap-frequency (-mgf) parameter controls the maximum proportion of stripped positions allowed per window before that window is skipped (default: 0.1). Windows that are skipped appear as gaps in the plot and as NaN in the CSV output.
• Base frequency estimation: For hky and tn93, base frequencies are estimated from the full alignment by default; per-window estimation can be enabled with --local-freqs (-lf) to capture local compositional variation along the genome.

Bug fixes

• Windowing fix: Windows are now guaranteed to contain exactly --windowsize sites. Previously, odd window sizes produced windows one site shorter than requested due to integer division. Windows are only emitted where a full window fits within the alignment; edge positions are no longer covered by truncated partial windows.

Full changelog: https://github.com/hodcroftlab/simplot-cl/commits/v1.0.4

SimPlot-CL v1.0.3

Release created primarily to fix remaining Zenodo issues.

What's Changed

• Updated Zenodo citation file

Full changelog: https://github.com/hodcroftlab/simplot-cl/commits/v1.0.3

SimPlot-CL v1.0.2

What's Changed

Added

• New arguments --width (-wd) and --height (-ht) to specify the dimensions of the output similarity plots. If not provided, default values are used (width: 14, height: 5).

Full changelog: https://github.com/hodcroftlab/simplot-cl/commits/v1.0.2

SimPlot-CL v1.0.1

Release created primarily to allow archiving on Zenodo (doesn't seem to be detecting previous release)

What's Changed

• Implemented mafft --auto alignment as default (skip with --no-align) by @kstrotjohann in #2

Full Changelog: https://github.com/hodcroftlab/simplot-cl/commits/v1.0.1

SimPlot-CL v1.0.0

This is the first public release of SimPlot-CL, a Python-based command-line tool for generating similarity plots (SimPlots) from nucleotide sequences.

SimPlot-CL enables automated and reproducible sliding-window similarity analyses, supporting:

• Command-line execution for batch processing
• Comparison of one or multiple query sequences against reference panels
• Optional alignment via MAFFT
• Customizable window and step sizes
• Flexible gap handling
• Metadata-based genotype annotation and color mapping
• Export of publication-ready plots and similarity tables