2004 days ago
2004 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...terman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA...2001 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
UPhO finds orthologs with and without inparalog...s usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO is a tree (or trees) in New...rs can be defined. Examples of trees to test UPhO are provided in the TestDat...2000 days ago
molinspiration: broad range of cheminformatics software tools supporting molecule manipulation
...spiration offers broad range of cheminformatics software tools supporting molecule manipulation...d drug design, high quality molecule depiction, molecular database tools supporting substructure and simil...1995 days ago
Osprey: Network Visualization System
...Stark, C., Tyers M. "Osprey: A Network Visualization System." Genome Biology 2003 4(3):R22 [Genome Biology] [PDF] [PubMed] and supported by the National In...1995 days ago
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
...d ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling...1995 days ago
1995 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...ith BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.1993 days ago
UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties
UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in...layout and introduces aggregates based on groupings and queries. The matrix l...ls about the original technique see the UpSet website. You can also chec...1986 days ago