Use MAFFT MSA Generation

The amino acid sequences corresponding to the proteins you want to generate an MSA for. This sequence will be used to find all matching sequences in the list of References Sequences defined below using phmmer.

List of amino acid sequences which you want to search for hits and create and alignment with the query sequence.

Top n number of sequences to keep in the output MSA. All other sequences will be dropped.

Set the maximum E-value threshold for sequence inclusion. Sequences with E-values above this threshold are excluded, allowing for more stringent or permissive search results. The E-value represents the expected number of matches with a given score due to chance alone, where lower values indicate higher significance. A default threshold of 1e-5 is commonly used for significant hits in bioinformatics searches. The minimum threshold of 1e-50 is for extremely stringent filtering, allowing only highly significant hits. Maximum threshold of 10 for very permissive filtering, potentially allowing less significant matches.