Add coalescent species tree pipeline as step 4astral (ASTER/ASTRAL-III)#83

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Alexdami17:custom-scripts

Commits on Jun 1, 2026

Add coalescent species tree pipeline as step 4astral
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README: add empirical guidance on --min_samples threshold for large datasets
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Make ASTER binary configurable via --astral_binary; auto-detect astral3/astral-pro3/astral-pro2
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README: document --astral_binary option and ASTER binary auto-detection
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Add wASTRAL and ASTRAL-IV support; include --abayes in per-gene IQ-TREE runs
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Fix stale astral3 references in aster.py and README
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Add --iqtree_model, --iqtree_args, --astral_args pass-through for step 4astral
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Refine ASTER binary descriptions in README
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Minor README formatting and phrasing cleanup in step 4 section
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Resume interrupted step 4astral runs by skipping completed gene trees
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Minor cleanup in --astral_args help text and docstring
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Minor README edits
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Add --no_fast flag; fix thread flag for IQ-TREE 2/3 compatibility
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Add --dna flag for DNA-based coalescent inference in step 4astral
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