Calculate allele frequencies from a sequence multialignment.
- Free software: MIT license
- Documentation: https://allfreqs.readthedocs.io
- GitHub repo: https://github.com/robertopreste/allfreqs
Calculate allele frequencies from a nucleotide multialignment in fasta or csv format.
Allele frequencies will be returned as a table in which each row is a nucleotide position (based on the provided reference sequence) and columns are A, C, G, T frequencies as well as gaps and other non-canonical nucleotides.
For example, given the following multialignment:
| ID | Sequence |
|---|---|
| ref | ACGTACGT |
| seq1 | A-GTAGGN |
| seq2 | ACCAGCGT |
the resulting allele frequencies will be:
| position | A | C | G | T | gap | oth |
|---|---|---|---|---|---|---|
| 1.0_A | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| 2.0_C | 0.0 | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 |
| 3.0_G | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |
| 4.0_T | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 |
| 5.0_A | 0.5 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 |
| 6.0_C | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |
| 7.0_G | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |
| 8.0_T | 0.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.5 |
Frequencies of non-canonical (ambiguous) nucleotides are by default squashed into the oth
column, but they can also be shown separately using a simple flag.
allfreqs can be used either as a command line tool or through its Python API.
For more information, please refer to the Usage section of the documentation.
PLEASE NOTE: allfreqs only supports Python >= 3.6!
The preferred installation method for allfreqs is using pip:
$ pip install allfreqsFor more information, please refer to the Installation section of the documentation.
This package was created with Cookiecutter and the cc-pypackage project template.