flutile 0.3.2

sequence analysis tools for flu research

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).