GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model (Ewens 1979). The purpose of this program is to simulate sequences on the whole genome scale within practical time. The program can be used to study the sampling properties of any statistics from a genome-wide study or to evaluate the performance of any method that is applied to genome-wide scale data.
“mRNA by SNP Browser” is an interactive package that provides graphical overviews of whole-genome association studies of datasets with very rich phenotypic information, such as global surveys of gene expression. The software incorporates a generic eQTL database and provides a graphic interface for browsing association between 54,675 transcript levels and 406,912 SNPs. For each transcript, our browser can tabulate and plot association test statistics (p-value<0.001), estimates of effect size and allele information across the genome. The browser automatically links results to the UCSC genome browser where users can examine each transcript in its genomic context. In addition to browsing the results by transcript or by position, results can be searched for information on specific SNPs. LD and tag information is provided for SNPs not in our database but evaluated by the International Hapmap Consortium.
MethylSig is our new R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments. Methylsig tests for differentially methylated sites (DMCs) or regions (DMRs) using a beta-binomial model to account for the coverage and variation among samples at each CpG site or region, and has a well-calibrated Type 1 error rate. Several options exist for either site-specific or sliding window tests, combining strands, filtering sites, and for local variance estimation. In addition, methylSig offers numerous functions for annotating and visualizing results, and testing for enrichment of overlap with the binding sites of transcription factors.
BSMAP（Bisulfite Sequence Mapping Program）is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.
The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.
wgd is a Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). wgd implements methods for constructing Ks distributions starting from a CDS fasta file, tools for intra-genomic synteny analysis and methods for modeling and visualizing Ks distributions.