BOL

github.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

www2.decipher.codes - DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL...

www.littlest.co.uk - Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological...

www.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...

bioconductor.org - doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...

Genetic variants discovery tool

broadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...

NCBI new updates !

Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina...

http://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...