Mafft - Align Sequences In Reference
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Align sequences (globally) in the reference fasta file to identify homology regions

**Location**

- *Filepath:* <SnakeLines_dir>/rules/shared/reference/alignment/mafft.snake
- *Rule name:* mafft__align_sequences_in_reference

**Input(s):**

- *reference:* Reference sequences in FASTA format

**Output(s):**

- *alignment:* Aligned sequences in ALN format

**Param(s):**

- *genbank_ids:* List of Genbank identifiers for sequences to download
- *email:* Inform NCBI who you are to contact you in case of excessive use. Otherwise they may block your access directly.