Input File

FluMut can analyze multiple A(H5N1) Influenza virus sequences simultaneously. It can handle partial and complete genome sequences of multiple samples. You must provide a single file containing all the nucleotide sequences in FASTA format (an example can be downloaded here). Sequences must adhere to the IUPAC code. FluMut relies on the FASTA header to assign the sequence to a specific segment and sample. For this reason, the header must contain both a sample ID (consistent among sequences of the same sample) and one of the the following segment names: PB2, PB1, PA, HA, NP, NA, MP, NS.

By default, the tool expects the sample ID followed by an underscore and the segment name (e.g. my_sample_PB2).

Custom FASTA header parsing

If your sequences have a different FASTA header composition, you can use the option --name-regex. This works with Python regular expressions, using a first capture group to find the sample and a second capture group to find the segment. Here we provide some examples with most common cases:

FASTA Header	Regular Expression
my_sample_PB2	(.+)_(.+)
my_sample|PB2	(.+)\|(.+)
my_sample-PB2	(.+)-(.+)
my_sample-PB2_something_else	(.+)-(.+?)_
PB2_my_sample	(?P<segment>.+?)_(?P<sample>.+)

To find the regular expression that better fits your FASTA header you can try it on Regex101 selecting Python flavor.

If in your fasta headers the segment label is located before the sample ID you can use named groups (sample and segment) as shown in the last row of the table.