Skip to main content

sequence analysis tools for flu research

Project description

Build Status



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 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 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:


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).

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for flutile, version 0.2.0
Filename, size File type Python version Upload date Hashes
Filename, size flutile-0.2.0-py3-none-any.whl (5.8 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size flutile-0.2.0.tar.gz (4.6 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page