omicR It creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence. These scripts can be used to run BLAST alignment of short-read (DArTseq data). It only works with BLAST V 2.7 or under.

A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis

A program used to find indels on target gene edited by CRISPR/Cas9

Mining NCBI BLAST output

omicR for R studio creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence. These scripts can be used to run BLAST alignment of short-read (DArTseq data) and long-read sequences (Illumina, PacBio… etc). You can use refer…

Automações para realizar alinhamentos em grande escala com o Blast

DNA barcoding analysis pipeline

various tools that help with deep sequencing analysis

PhylUp - a python package to automatically generate alignments (or update alignments and phylogenies) using local sequences or a local Genbank database while controlling for the number of sequences per OTU.

BLAST searches in parallel using GNU Parallel

Parser of BLAST results

Pipeline to create phage genome synteny graphics from genbank files

Map SNP positions to a supplied reference assembly using BLAST. Filter results for best hit. Output in plink format.

MIP_ORACLE: Identifies unique target regions with diagnostic significance in pathogens.