Table 3.

Description of software packages used in this study, including operating systems, important features, URL where software can be obtained, number of citations, authors, and brief comments describing the ease of use.

Software	Operating system	Features	URL	Citations (Web of Science/Google Scholar)	Reference	Comments
Geneious	Linux, Mac OSX, Windows	Integrates multiple functions with plugins, user-friendly interface	http://www.geneious.com/features/microsatellite-analysis	395/633	Kearse et al., 2012	Very user friendly, but requires a paid license to run. The microsatellite development plugin (Phobos, http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm) is freely available, very easy to use, and quick.
GMATo	Linux, Mac OSX, Windows	Both GUI and command line interface; SSR mining and statistics at genome level	http://sourceforge.net/projects/gmato/files/?source=navbar	0/8	Wang et al., 2013	Runs quickly and has clear output, but it is hard for the user to change important parameter settings.
HighSSR	Linux, Mac OSX, Windows	A Java program is designed for NGS data and capable of microsatellite detection, elimination of redundancy and primer development, and interacting with PostgreSQL, MUSCLE, and Primer3.	https://code.google.com/p/highssr/	7/12	Churbanov et al., 2012	Cannot open large files (>2 GB); unsuitable for most NGS data.
MISA	Linux, Mac OSX, Windows	Preprocessing sequences, motif search, and interacts with Primer3 for primer designs	http://pgrc.ipk-gatersleben.de/misa/	669/1150	Thiel et al., 2003	Fast, easy to configure, generates primers.
MSATCOMMANDER	Linux, Mac OSX, Windows	Motif search, interacts with Primer3 for primer design, and primer auto-tag	http://code.google.com/p/msatcommander/	428/509	Faircloth, 2008	Output is difficult to view; requires lots of filtering to find basic statistics.
PAL_FINDER	Linux, Mac OSX, Windows	Identifies and characterizes microsatellite repeat loci from shotgun genomic sampling by 454 or Illumina paired-end reads, and designs PCR primers by interacting with Primer3	http://sourceforge.net/projects/palfinder/ or http://www.snakegenomics.org/CastoeLab/Software.html	87/115	Castoe et al., 2012	Slow, struggles with large files; compatibility issues with many FASTQ formats; would not complete with the largest data set.
QDD3	Windows and Linux	A computer program to select microsatellite markers from raw sequence reads obtained from 454 or Illumina and design primers from large sequences at genomic level, dealing with the essential bioinformatics and equipped with both command line and a user-friendly graphical interface on the Galaxy server.	http://net.imbe.fr/∼emeglecz/qdd	3/9	Meglécz et al., 2014	Relatively long running time; user cannot easily change parameter settings.
SSR Locator	Windows	Integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, PCR simulation, global alignments, and identity and homology searches; eliminates overlaps between adjacent sequences; interacts with Primer3	http://www.hindawi.com/journals/ijpg/2008/412696/	0/98	Da Maia et al., 2008	Requires tedious file reformatting; only available for Windows.
SSR_pipeline	Linux, Mac OSX, Windows	Identifies simple sequence repeats, e.g., microsatellites from paired-end high-throughput Illumina DNA sequencing data	http://pubs.usgs.gov/ds/778/	3/3	Miller et al., 2013	We could not get it to run after ∼24 h of effort.
STAMP	Linux, Mac OSX, Windows	Based on STADEN package, with comprehensive integration of a set of extension modules to facilitate the processing of microsatellite markers, like Phobos, TROLL, Primer3, SQLite module.	http://www.awi.de/en/research/scientific_computing/bioinformatics/software/	11/15	Kraemer et al., 2009	Powerful, but not user friendly. Other modules associated with it (Phobos) quickly and conveniently locate potential loci.