E

Fast genome-wide functional annotation through orthology assignment.

The EIGENSOFT package implements methods for analzing population structure and performing stratification correction

elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.

ELSA - Finding Time-Dependent Associations (Now Augmented with Liquid Associaiton)

Fast & accurate alignment of barcoded short-reads.

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

The European Molecular Biology Open Software Suite

Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI).

A collection of scripts to assist in the retrieval of data from the ENA Browser

Ensembl Variant Effect Predictor

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

A pipeline and a framework for NGS analysis (RNA-Seq and Chip-Seq)

Massively parallel phylogenetic placement of genetic sequences

ChIP-seq broad peak calling tool, meant to be easier to use and more performant than SICER

A Python framework for reconstructing, analysing and visualizing phylogenetic trees and multiple sequence alignments. Includes Python API and Phylogenomic tools

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Exonerate - A generic tool for pairwise sequence comparison / alignment