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ms (Dick Hudson) Data File Format
See Also: Input Data Files Output
References: Hudson 2002
This command allows exporting the data (intraspecific data) on the ms file format (Hudson 2002). This format can
be read (among others) by some of Hudson (see Hudson 2002) and Kim programs:
Kim, Y. & Stephan, W. (2003): Selective sweeps in the presence of interference among partially linked loci.
Genetics, 164:389-398.
Kim, Y. & Stephan, W. (2002): Detecting a local signature of genetic hitchhiking along a recombining
chromosome. Genetics 160: 765-777.
Data Files:
For the present analysis, at least one set of sequences must be defined (see: Data | Define Sequence Sets
command).
Analysis using one sequence set. The sequence set must include intraspecific data information. DnaSP will
estimate some measures of the extent of DNA polymorphism.
Analysis using two sequence sets (interspecific data). One Sequence Set must contain the intraspecific
data, while the other must contain sequences (one or more) from an outgroup (DNA data from a different species
or a different population); in this case DnaSP will use the first sequence to polarize substitutions.
Alignment gaps and missing data:
Sites with alignment gaps or missing data in any data file are not used, i.e. these sites are completely excluded.
Implementation:
Sites with three of four nucleotide variants will not be used. Sites with ambiguous information in the outgroup (if
this option is chosen) will also not be used.