1) FindGSE: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model. The current version works on Linux & Mac OS X with R version 3.3.1 or above. For more details, please visit FindGSE.
3) QTCat: All SNPs are jointly associated to the phenotype and at the same time correlation among them is considered. Thus, correction for population structure becomes unnecessary, which in many cases results in a power advantages compared to other methods.
4) SHOREmap v3.x (latest v3.5): Whole genome resequencing of pools of recombinant mutant genomes allows directly linking phenotypic traits to causal mutations. Such an analysis, called mapping-by-sequencing, combines classical genetic mapping and next generation sequencing by relying on selection-induced patterns within genome-wide allele frequency in pooled genomes. SHOREmap is a computational tool implementing a method that enables simple and straightforward mapping-by-sequencing analysis. For more details, please visit SHOREmap.
1) SyRI: Advances in sequencing technologies have led to easy and quick generation of high quality genomic assemblies, which can be used to answer the elementary question of identifying genomic differences between organisms. Synteny and Rearrangement Identifier (SyRI) uses whole genome alignment (generated by MUMmer) to find the best syntenic path between the genomes as well as identify various large structural rearrangement (inversion, duplication, and translocation) present between the two genomes. Apart from this SyRI also identifies structural variations and allows easy identification of meaningful SNPs (assisted MUMmer).