DnaSP

DnaSP or DNA Sequence Polymorphism, is a Java-based application designed to help you with the analysis of nucleotide polymorphism. The DNA polymorphism is a scientific term that refers to the differences in the nucleotide sequence between individual, distinctions that can take on many forms, from single base pair changes to alterations in the number of copies in a given DNA sequence.

The program is designed to help scientists and students alike make estimations of the DNA sequence variations within and between populations. At the same time, it can be useful for studying linkage disequilibrium, recombination, gene conversion and gene flow as well as several perform neutrality tests.

The tool comes with a plethora of specialization tests and analysis, including Tajima Test, Fu and Li's (and Other) Tests, Gene Conversion, Synonymous and NonSynounymous substitutions, InDel or Insertion-Deletion Polymorphism or Conserved DNA Regions, just to name a few. Other tools worth mentioning include Evolutionary Calculator, Discrete Distributions, HKA test (Direct Mode), Test of Independence 2×2 table as well as various Coalescent Simulations.

With the help of the program you can generate DNA Sliders, Haplotype Data File, Reverse Complement Data File, ms (Dick Hudson) Data File Format, Concatenate Data Files, Reverse Complement Data File and Translate to Protein Data file.