SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a...2321 days ago
2315 days ago
zPicture: A dynamic blastz alignment visualization
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.2280 days ago
xmatchview: smith-waterman alignment visualization
...gn 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats...nux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (199...2314 days ago
Seal: SEquence ALignment evaluation suite
...is a comprehensive sequencing simulation and alignment tool evaluation suite. This s...veral utilities that can be used to evaluate alignment algorithms, including: Rea...encing error rate, and indel rate. Applying alignment tools to the genome and the r...2308 days ago
LRCstats: Long Read Correction Statistics
...s produced by simulators (such as SimLoRD or PBSim) where the two-way alignments between the uncorrected long...ing sequences in the reference genome (Ref) are given in some sort of alignment file and then aligning the co...2306 days ago
PGAP-X: Extension on pan-genome analysis pipeline
...rvative levels, and genetic variation from pan-genome sight. At the same time, analytical result data from many other programs, including genome alignment result and orthologs clusters...2288 days ago
MUMmer4: A fast and versatile genome alignment system
...biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes; ...2277 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
...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), and synteny). One is c...843 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sens...mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost...2196 days ago