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Add support for alternate genetic codes

enhancementNew feature or requestNew feature or request

Status: Open.

#18 In veg/CAPHEINE;

· hverdonk opened on Dec 5, 2025

Add a check to make sure reference gene sequences are a multiple of 3.

enhancementNew feature or requestNew feature or request

Status: Open.

#17 In veg/CAPHEINE;

· hverdonk opened on Nov 13, 2025

Implement support for paralog handling

enhancementNew feature or requestNew feature or request

Status: Open.

#14 In veg/CAPHEINE;

· hverdonk opened on Oct 16, 2025

Implement support for recombination detection & analysis

enhancementNew feature or requestNew feature or request

Status: Open.

#13 In veg/CAPHEINE;

· hverdonk opened on Oct 16, 2025

Skip analyzing genes with internal stop codons

enhancementNew feature or requestNew feature or request

Status: Open.

#12 In veg/CAPHEINE;

· hverdonk opened on Oct 16, 2025

Feature Request: Allow hyphy analyses to be run on pre-prepared data

enhancementNew feature or requestNew feature or request

Status: Open.

#5 In veg/CAPHEINE;

· hverdonk opened on May 22, 2025

Bug: Foreground sequence IDs fail to match due to sanitization and deduplication

bugSomething isn't workingSomething isn't working

Status: Open.

#1 In veg/CAPHEINE;

· hverdonk opened on May 22, 2025