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...
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...
www.cmbb.arizona.edu - CrusView is a java based tool for karyotype/genome visualization and comparison of crucifer Species. It also integrates an binary version of KGBassembler and a post-modification step for its assembling result.
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...
www.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...
bioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...
http://assemblytics.com/ - Download and install MUMmer
Align your assembly to a reference genome using nucmer (from MUMmer package)
$ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
Consult the MUMmer manual if you encounter problems
Optional: Gzip...
bioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...
http:--www.biotechnology.jhu.edu-
Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the
Basic Local Alignment Search tool and will protein and DNA sequences that
are...
bioinfo.lifl.fr - YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST,...
