IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelih...he IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100%...1952 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 bi...viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number...1916 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency of chr...been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chro...1889 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1794 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...les. Miropeats enhances the utility of conventional DNA sequence comparisons when loo...1762 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://aide...1602 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/PMC4086085/1602 days ago
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