“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retr...2167 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...NA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding an...structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to...2159 days ago
Digest: In silico restriction digest of complete genomes
This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragment...2188 days ago
CGView - Circular Genome Viewer
...L file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends...2150 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...en two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies....ppings and alignment identity estimates. Based on our experiments with complete and draft genomes, its accura...2127 days ago
Bokeh: An interactive visualization library that targets modern web browsers for presentation
...make your visualizations, see the User Guide. To see examples of how you might use Bokeh with your own data, check out the Gallery. A complete API reference of Bokeh is at&...2099 days ago
S-plot2: creates an interactive, two-dimensional heatmap of sequences
...an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryoti...2051 days ago
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
...an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryoti...2046 days ago
vcfR: a package to manipulate and visualize VCF data in R
...nformation can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF...2024 days ago
BLAST options, setting and defaults
...BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST. A fairly complete on-line guide to BLAST search...1978 days ago