BOL

prakharg24.github.io - We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have...

harvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...

github.com - xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and...

github.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...

BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn  -query genes.ffn  -subject genome.fna  -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident...

It's been a while since I last installed BLAT and when I went to the download directory at UCSC: http://users.soe.ucsc.edu/~kent/src/ I found that the latest blast is now version 35 and that the code to download was: blatSrc35.zip....

github.com - SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web. More at http://sequenceserver.com.

github.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...

github.com - Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors. When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly,...

mulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...