DnaSP version 5.0
Julio Rozas et al.
1) Possibility to reconstruct haplotypes from Unphase/Genotype data. The Haplotype reconstruction is conducted using the algorithms provided in PHASE, fastPHASE and HAPAR.
2) Analysis of Insertion/Deletion (InDel) Polymorphisms (DIPs).
3) Estimation of the normalized Fay and Wu's H test statistic.
4) Possibility to automatically read and analyse (intraspecific and interespecific variation) multiple data files sequentially (as a Batch mode).
5) Identification of conserved DNA regions (this feature might be useful for phylogenetic footprinting-based analyses).
6) Possibility to Read HapMap3 format files with phased haplotypes.
1) Possibility to define set of functional regions. Store that information on NEXUS files. Analysis in functional regions.
2) Possibility to display the DNA sequence data, and sliding window results, integrated with available genome annotations using the UCSC browser. This feature is interesting for species with completely sequenced genomes. The genome annotation information (genome information, position coordinates) can be stored on NEXUS data files.
3) Compatibility with Windows Vista.
4) Possibility to automatically read and analyse (intrespecific variation) multiple data files sequentially (as a Batch mode). These data files can contain different number of sequences, or include different genomic regions.
5) New Help File.
1) New Interface.
2) Possibility to define set of sequences. Store that information in NEXUS files. Analysis in set of sequences.
3) Increase the length of the DNA sequence to be analyzed (until ~5 Mbp).
4) Extensive Coalescent Simulation analyses.
5) Estimation of Gene Flow between and among populations.
6) Testing for Genetic Differentiation (Permutation test).
7) Analysis of preferred and unpreferred synonymous codons. Possibility to define synonymous codon preference tables. Store codon preferences information in NEXUS files.
8) Estimation of new test statistics (Fay and Wu's H; Rozas et al.'s ZZ; Ramos-Onsins and Rozas R2; and more). Analysis of Fay and Wu's H by sliding window.
9) Analysis of Pi(a)/Pi(s) and Ka/Ks ratios by the sliding window method.
10) New Predefined Genetic Codes.
11) Possibility to create an Arlequin project file (*.arp) with haplotype data information.
12) Possibility to create a concatenated data file (NEXUS format) including DNA sequence information from a number of single files.
and References on DnaSP
April 15, 2009
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