PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), an...891 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a...alignment so that it becomes more suitable for phylogenetic analysis. This s...lected from a protein alignment. Further information can be found in the onli...2206 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an onli...2197 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate singl...d generates concise comparison of enzyme(s) performa...ation, please see the academic paper published onli...2196 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 &&am...a ./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam #...q.gz > aln.sam # Oxford Nanopore genomic reads ./min...pore read overlap # man page for detailed command line options...2188 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2056 days ago
2016 days ago
regioneR: an R package for the management and comparison of genomic regions
Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for b...icRanges and a powerful and customizable permutation test framework. With it, it's poss...2014 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab...ganization that includes MAKER, has some nice tutorials online for r...e were quite simplified examples and it took a bit of effort...2005 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an importan...expressed, we should expect a positive association. Similary, we can perform...1997 days ago