ReadTools provides a consistent and highly tested set of tools for processing sequencing data from any kind of source and focusing on raw reads, while including tools for mapped reads as well. Diverse formats were developed for storing reads, but ReadTools opt for following the SAM specs to maintain a common data format to store both raw/mapped reads. Thus, ReadTools also helps to standardize sequencing data in different formats.
SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.
poolSeq is an R-package that allows you to analyze and simulate Pool-Seq time-series data. Its functionality includes estimation of the effective population size and quantification of selective strength, as well as dominance. Besides simulating Pool-Seq data under a specific scenario, you can also load empirical data into R using the common sync-file format (see PoPoolation2).
PoPoolation is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals
PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution
PoPoolation DB provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.
PoPoolationDB database for three Drosophila species:
PoPoolationTE2 enables comparative population genomics of transposable elements (TE). As a major innovation PoPoolation TE2 introduces the physical pileup file which allows to homogenize the power to identify TEs and thus enables an unbiased comparison of TE abundance between samples, where samples could be pooled populations, tissues or sequenced individuals.
Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.
ModifyMaxLkAndPairwise is an R-package for improving the output of the max_lk function of LDhelmet and the pairwise function of LDhat in terms of the mean squared error by rescaling it with a certain constant as described in K. Gärtner and A. Futschik: Improved Versions of Common Estimators of the Recombination Rate. J Comp Biol 23(9):756-68 (2016).
MimicrEE is a tool for simulating genotypes and phenotypes in experimentally evolving populations.
MimicrEE is a forward simulation tool of standing genetic variation, thus no 'de novo' mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.
Allim (Allelic imbalance meter) offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.
DistMap is a toolkit for distributed short read mapping on a Hadoop cluster.
Microsatellite Analyzer (MSA) provides basic summary statistics for microsatellite data. Written by Daniel Dieringer
ms2ms.pl converts the output of Hudson's makesample software into microsatellite data. The output could be directly analyzed by MSA. Written by Sreenivasa Rao Pidugu
CANGS1.1 a user-friendly utility for processing and anylyzing 454 GS-FLX data in biodiversity studies. Written by Ram Vinay Pandey
CANGSdb is a stand-alone web-based database tool for processing, managing and analyzing 454 sequencing data in biodiversity studies.