Overview

Analysis of nucleotide polymorphisms in populations determines the relative contributions of mutation, random genetic drift, natural selection, recombination, and migration in shaping genetic diversity. DnaSP 3.50, DNA Sequence Polymorphism, is a software package that geneticists can use to estimate nucleotide variation within and between populations using sequence alignments supplied by the user.

DnaSP has five major program modules: Display, Analysis, Overview, Tools, and Data. The Display module allows the user to look at the aligned sequence data and highlight various types or groups of nucleotides such as codons, polymorphic sites, or alignment gaps. The Analysis module can estimate the neutral mutation, recombination, and migration parameters from polymorphism data to assess the past action of these forces in the history of the sequence sample. This module also allows one to test pairs of nucleotides for statistical association or to test the DNA region for past gene conversion events. The Analysis module can be used to perform four statistical tests of the neutral mutation hypothesis. Departures from the neutral mutation hypothesis indicate the past action of natural selection in the DNA region being studied. The Overview module allows the user to get a quick summary analysis for gene region. This analysis will display the number of segregating sites, pairwise differences, and haplotypes, and several tests of the neutral mutation hypothesis. The Tools module has a number of utilities useful to the evolutionary biologist, such as an evolutionary calculator, a 2 x 2 contingency test utility, and a coalescent simulation module. The Tools module adds considerable power because it allows the investigator to determine confidence intervals for many of the parameters estimated within the Analysis module of DnaSP and to perform common statistical tests used in population genetics. The Data module allows the user to specify what types of data will be used in the Analysis module of the program. For instance, one can choose to use or not use alignment gaps in some analyses. One can specify coding regions within this module using either the universal genetic code or a user-specified genetic code. One can generate subsets of the original data set either as subsets of individual sequences or as subsets of nucleotide sites. The ability to select different sets of sequences or sites and save the subsets makes this program quite versatile and gives the user a great deal of flexibility to be creative in the analysis of data.

How Long Did It Take to Learn to Use It Productively?

I am a classic "I don't need manuals" kind of person when it comes to using software. I installed DnaSP and started to run the analyses. DnaSP can be installed and used very quickly provided one has data in an appropriate input format used by the program. If one has little training in population genetics, then the interpretation of the results of this program will require far more time than the time needed to learn how to use the program.

Product Quality

Customizability

Not applicable.

Ability to Program in Scripts, Add Extension Modules, etc.

Not applicable.

Ability to Import and Export in Different File Formats

The input and output formats used by DnaSP are standard formats used in genetic databases and phylogenetic-analysis software. Other software is required to generate the aligned-sequence file, but many programs used by genetic databases use the FASTA or NEXUS formats. DnaSP automatically inputs or exports sequences in any one of the following five file formats: MEGA, NBRF/PIR, NEXUS, FASTA, and PHYLIP. The output of analyses is displayed in windows with text, tables, spreadsheets, or graphs. Output can either be sent to the printer (any Windows printer driver) or saved in a file.

Useful or Unusual Features

Many of the routines generate graphical output that can help the user visualize complex patterns in aligned sequences. One particularly useful graphic can be generated within the linkage-disequilibrium module, which plots a variety of measures of statistical association between nucleotides and nucleotide distance between sites. The user can choose to plot significant linkage-disequilibrium values versus nonsignificant values.

Limitations

DnaSP does not have many tools to manipulate the graphical output to generate publication-quality figures. The program is designed specifically for population genetic analysis of nucleotide sequences and not for analyses of other types of molecular genetic markers such as allozymes, RFLPs, AFLPs, or microsatellites. While this may be a limitation, it is not a major criticism because the software was created for very specific population genetic analyses. There is a limit on the size of the nucleotide-sequence data set that can be imported into DnaSP in terms of number of sequences and number of nucleotides per sequence. However, in practice this is no limitation at all because the largest data sets generated to date do not approach the limits of the current hardware and software.

Comparisons with Similar Software

The Arlequin program is likely to be the closest competitor for DnaSP. I downloaded Arlequin a number of years ago to give it a try and did not have much luck with the program. Truth be told, I did not give it sufficient time to judge realistically the merits of Arlequin. The documentation for Arlequin suggests that the program does far more types of analyses than DnaSP, but the learning curve for Arlequin seemed steeper in comparison to DnaSP.

Technical Support and Documentation

The documentation for DnaSP is outstanding. The program provides standard Windows help menus that allow the user to view help under major categories or through an index window. The help menu also provides extensive citations to the primary population genetics literature, which can provide the newest student of population genetics with a primer to the most influential papers in the field. I have not needed technical support for the program, but I do know that Julio and Ricardo Rozas have been diligent in their efforts to fix bugs and add new features to the program. Over the last five years, the Rozas have produced three major versions of DnaSP and several minor updates to the program. Each new version has been better than the previous version; bugs have been repaired and many new features have been incorporated. Even though the authors are not receiving major compensation for this program, they have kept the analyses in the program accurate and state-of-the-art. This provides insight into the technical support that is available for the software.

Target Users

Molecular population geneticists, molecular evolutionary geneticists, molecular geneticists.