# eggnog-mapper

**Repository Path**: all_create_code/eggnog-mapper

## Basic Information

- **Project Name**: eggnog-mapper
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: AGPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-08-11
- **Last Updated**: 2021-11-09

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

[![Build Status](https://travis-ci.com/eggnogdb/eggnog-mapper.svg?branch=master)](https://travis-ci.com/eggnogdb/eggnog-mapper)
[![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=eggnog_mapper)

# Overview
**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.

Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).

Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb).

EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de

# Documentation
https://github.com/jhcepas/eggnog-mapper/wiki

# Citation

If you use this software, please cite:
```
[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
    prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
    Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
    Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
    orthology resource based on 5090 organisms and 2502 viruses. Jaime
    Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
    K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
    J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
    47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 
```

Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction:
```
[HMMER] Accelerated Profile HMM Searches. 
        Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.

[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND.
          Buchfink B, Reuter K, Drost HG. 2021.
          Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x

[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
          Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988

[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification.
           Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119.

```