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Matrix Maker

Matrix Maker is a simple but handy utility to download DNA sequences from GenBank and construct alignments when the taxa (with or without synonyms) and gene regions of interest are already known.


Freyman, W.A. and A.H. Thornhill. 2016. Matrix Maker [Computer software]. Retrieved from

Other stuff:

Copyright 2016 Will Freyman -
License: GNU GPLv3


Python 2.7
MAFFT v6.9+

Quick usage:

python -e -g example/genes.csv -m 5000 -s example/synonyms.csv

Detailed usage:

usage: [-h] [--email EMAIL] [--genes GENES]
                       [--max_seq_length MAX_SEQ_LENGTH] [--species SPECIES]
                       [--taxids TAXIDS]

optional arguments:
  -h, --help            show this help message and exit
  --email EMAIL, -e EMAIL
                        Email address for NCBI database searches.
  --genes GENES, -g GENES
                        Text file that defines the gene regions of interest
                        using both include and exclude terms.
  --max_seq_length MAX_SEQ_LENGTH, -m MAX_SEQ_LENGTH
                        Optional. Sets the maximum sequence length to include.
                        Use this to exclude genomes.
  --species SPECIES, -s SPECIES
                        Text file that contains a list of all species
                        binomials and their synonyms.
  --taxids TAXIDS, -t TAXIDS
                        Optional. Text file that contains a list of all
                        taxids. Use this to avoid repeating the NCBI taxid