2047 days ago
RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by p...2034 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly...It is a very fast search algorithm that is used to separately search protein or DNA da...1988 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows t...e-made tabular files. Features Linear representation of several segments of DNA C...1986 days ago
FGENESH - Program for predicting multiple genes in genomic DNA sequences
FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing...1978 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compare...the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA al...1918 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimenta...viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA bi...1883 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when ce...e been recognized as a preferential site for integration of exogenous oncogenic DNA vi...1855 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1761 days ago
Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically....t presentation styles. Miropeats enhances the utility of conventional DNA se...1728 days ago