splitmsa/README.md

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# SplitMSA
2023-03-22 19:30:53 +00:00
Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.
2023-03-22 20:13:37 +00:00
## Features
- Split large fasta files that contain a multiple sequence alignment (MSA) into individual genes
- Trim off stop codon
- Batch process multiple genes from one MSA
- Correct gene start and stop locations based on start and stop codon location
- Catalogues errors that occurred in human-readable CSV file
## Planned
- Translate MSA into amino acids while maintaining alignment (shows type of mutation if frameshift)
- Simple to use GUI
- Run without system-wide python install
## Use
### Command Line
1. Install python 3
2. Install `biopython`
- Using `pip`: `pip install biopython` or `pip3 install biopython`
- Using `conda`: ` conda install -c conda-forge biopython`
3. Download `msa_splitter.py` and run with `python3 msa_splitter.py`
- `python3 msa_splitter.py -h` for help