sequence analysis tools for flu research
Project description
flutile
Installation
pip install flutile
Commands
compare
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
output:
site | A | B | C | D | E | F | G | H |
---|---|---|---|---|---|---|---|---|
2 | L | M | M | M | M | M | ||
12 | N | I | I | I | T | T | I | T |
66 | T | K | ||||||
110 | S | P | P | P | P | P | ||
116 | T | A | ||||||
140 | K | R | R | R | R | R | ||
146 | K | E | E | E | E | |||
147 | K | M |
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 (--make-consensus
and
--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
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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