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 in...2033 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et...It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used...1987 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene...e-made tabular files. Features Linear representation of several segments of DNA Comparisons represented by a...1985 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 sequenci...1977 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum lik...the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100%...1917 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 variou..., viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number...1882 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency of...e been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chro...1854 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1760 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 t...yles. Miropeats enhances the utility of conventional DNA sequence comparisons when loo...1727 days ago
1587 days ago