splitmsa/README.md

SplitMSA

Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.

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