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IQ-TREE DNA autodetection is failing

Status: Open.

#91 In aineniamh/squirrel;

· Eddylusamaki opened on Apr 9, 2026

Add 'how to cite' to README

Status: Open.

#86 In aineniamh/squirrel;

· rambaut opened on Dec 6, 2025

Error with --run-apobec3-phylo option : reconstruction.smk [?]

Status: Open.

#82 In aineniamh/squirrel;

· Nicolas-Fernandez opened on Sep 29, 2025

Flatten IUPAC ambiguity codes to Ns

Status: Open.

#81 In aineniamh/squirrel;

· rambaut opened on Aug 20, 2025

dont add og to alignment until iqtree step

Status: Open.

#77 In aineniamh/squirrel;

· aineniamh opened on Jun 26, 2025

Tree string unparseable

Status: Open.

#75 In aineniamh/squirrel;

· MarliesJFrancine opened on Jun 17, 2025

sequences dropped during alignment

Status: Open.

#72 In aineniamh/squirrel;

· NikitaSitharam opened on May 20, 2025

xml for BEAST analysis

Status: Open.

#63 In aineniamh/squirrel;

· lingxuan85511 opened on Dec 5, 2024

Apobec analysis on existing tree

Status: Open.

#62 In aineniamh/squirrel;

· MarliesJFrancine opened on Nov 26, 2024

inter-clade alignment

Status: Open.

#44 In aineniamh/squirrel;

· aineniamh opened on Sep 20, 2024

mutations for each sample as an output for Squirrel

Status: Open.

#38 In aineniamh/squirrel;

· aineniamh opened on Sep 18, 2024

tackle interclade alignment, but also with appropriate masking flags (snps and alignment issues that don't look quite right

Status: Open.

#34 In aineniamh/squirrel;

· aineniamh opened on Sep 6, 2024