sequence analysis tools for flu research
pip install flutile
compare takes a multiple-sequence alignment as an input and creates a
character difference table. This command is designed for preparing amino acid
difference tables (although it will accept DNA as well). Below is an example
Sequences B-H are compared to sequence A. Every difference is reported with the alternative amino acid, while identities are left blank.
compare takes two arguments (
--use-consensus-as-reference) which will add a consensus column as the final
column in the table of as the first (in which case it is the reference column).
represent takes a multiple-sequence alignment as input and removes entries
that are similar in sequence and time. The function requires that headers have
a date term (with format year/month/day). For example:
>A|1990-01-02 GATACA >B|1990-02-02 CATATA
There may be gaps in the alignment. Sequences in the alignment that are
separated by less than or equal to
--max-day-sep and that are a sequence
identity of greather than or equal to
--min-pident-sep will be clustered
together. A single representative is sampled from each cluster (the latest one
with ties resolved by order).
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