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README.md
matrix_maker.py

README.md

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.

Citation:

Freyman, W.A. and A.H. Thornhill. 2016. Matrix Maker [Computer software]. Retrieved from https://github.com/wf8/matrixmaker

Other stuff:

Copyright 2016 Will Freyman - freyman@berkeley.edu
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html

Requirements:

Python 2.7
Biopython
MAFFT v6.9+

Quick usage:

python matrix_maker.py -e your_email@here.edu -g example/genes.csv -m 5000 -s example/synonyms.csv

Detailed usage:

usage: matrix_maker.py [-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
                        lookups.