Changelog

1.1.7 January, 2026

• New function: Steps control in stage 4
  • Added support for controlling individual steps within Stage 4, allowing users to selectively run specific steps (e.g., gene tree inference, alignment trimming, species tree inference) rather than executing the entire stage in one go. here for details.

1.1.6 September, 2025

• New dependency: Plotly
  Plotly has been integrated into the new script plot_recovery_heatmap_v2.py to generate an interactive HTML heatmap visualizing target locus recovery in Stage 2. This heatmap provides useful guidance for parameter selection in Stages 3–4.

• TreeShrink integrated into Stage 3
  TreeShrink has been incorporated into Stage 3 as an optional processing step. Users can enable it by setting the option -run_treeshrink to TRUE. TreeShrink removes genes with excessively long branches and is available for all seven paralog-handling pipelines except ParaGone, as TreeShrink is already implemented within the ParaGone pipeline.

1.1.5 September, 2025 - MAJOR UPDATE !

• Pipeline restructuring

  • Stage consolidation: Combined previous stages 3 and 4, simplifying the pipeline from 5 to 4 stages.
  • Stagewise execution: Added flexible stage-by-stage execution capability.

• Enhanced functionality
  Gene tree inference:

  • Added support for IQ-TREE and FASTTree.
  • Deprecated RAxML.

  Alignment trimming:

  • New alternative: Integrated HMMCleaner
  • Maintained trimAl as the default setting.

  Species tree inference:

  • Added ASTRAL-pro3 for multi-copy gene aware coalescent analysis.

1.1.3-1.1.4 August, 2025

Fixed some bugs in stages control. These versions have been abondoned.

1.1.2 August, 2025

Integrated ASTRAL-IV into the pipeline stage 4.

Usage Update:

• Run ASTRAL-IV with parameter: -tree 4

New dependency:

• ASTER(conda version)

1.1.1 August, 2025

Fixed some common bugs.