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 https://github.com/wf8/matrixmaker
Python 2.7 Biopython MAFFT v6.9+
python matrix_maker.py -e firstname.lastname@example.org -g example/genes.csv -m 5000 -s example/synonyms.csv
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.