2326 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2300 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference gen...1580 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
...mes its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensit...MMseqs2 user guide is available as Github Wiki or as PDF file (Thanks to pandoc!)...2278 days ago
ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
...e for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic analysis: RAxML, File Converter, MS Comparison, and...2279 days ago
2235 days ago
CrossMap: a program for convenient conversion of genome coordinates
...a program for convenient conversion of genome coordinates (or annotation files) between different assemblie...mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wi...2208 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
...onality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks selec...2206 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
...ion. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an...ay dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.i...2197 days ago
2194 days ago