IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compar...he IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA align...1915 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 bindi...1880 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 c...been recognized as a preferential site for integration of exogenous oncogenic DNA virus...1852 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1758 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....presentation styles. Miropeats enhances the utility of conventional DNA seque...1725 days ago
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3D de novo assembly (3D DNA) pipeline
For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenla...1566 days ago
DMINDA2: an integrated web server for DNA motif identification and analyses
DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses More at http://bmbl.sdstate.edu/DMINDA2/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/1566 days ago
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