haplotype frequencies. Also it can run tests of departure from
linkage equilibrium and do thorough analyses of population subdi-
vision under the AMOVA framework.
When imported data is in the RFLP data:“1” means there exist restriction sites, while “0” means none, and
“-” means a lack of restriction sites.When imported data is DNA sequences:“-” stands for a lack of nucleotide, while “?” stands for an unknown
nucleotide.
“R” means A/G (purine), while “Y” means C/T (pyrimidine).
“M” means A/C, “W” means A/T; “S” means C/G, “K” means
G/T, “B” means C/G/T, “D” means A/C/T; “H” means
A/C/T; “V” means A/C/G; “N” means A/C/G/T.2.3.3 DnaSP It is a software for comprehensive analysis of DNA polymorphism
data. As a powerful tool, it helps us to understand the evolutionary
process and to establish the functional significance of particular
genomic regions [7].
Remarkably, the DnaSP v5 can handle and analyze multiple
data files in batch. It can identify conserved DNA regions, which
can contribute to phylogenetic footprint-based analysis. Also, it
allows exhaustive DNA polymorphism analysis, and the results
can be illustrated graphically and in a text format.
2.3.4 SSAHA2 (Sequence
Search and Alignment by
Hashing Algorithm)
It is a pairwise sequence alignment program designed for the
efficient mapping of sequencing reads onto genomic reference
sequences.
It can recognize a range of output formats concluding SAM,
CIGAR, PSL, etc. And this tool reads data from most sequencing
platforms like ABI-Sanger, Roche 454, and Illumina-Solexa.
There are many other tools for researchers to use, facilitating
them to better analyze data generated. Table2 illustrates tools of
different kinds.3 Extension: Methods and Tools for DNA Sequence Analysis
3.1 Background In the past decades, many manual methods have been applied to
analyzing DNA sequence data. However, the drawbacks of these
methods are apparent—when the data is in extraordinary amount,
it takes lots of time and energy. Fortunately, computers are well-
used in solving the problem. By establishing DNA sequence data-
bases storing data information of magnanimity, researchers are able
to adopt statistical approaches for analysis.
8 Keyi Long et al.