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README.mdH A D25-Oct-20212.9 KiB6047

README.md

1![diamond](http://www.diamondsearch.org/diamond_white_95px.png)
2
3Introduction
4============
5
6DIAMOND is a sequence aligner for protein and translated DNA searches,
7designed for high performance analysis of big sequence data. The key
8features are:
9
10-   Pairwise alignment of proteins and translated DNA at 100x-10,000x
11    speed of BLAST.
12-   Frameshift alignments for long read analysis.
13-   Low resource requirements and suitable for running on standard
14    desktops or laptops.
15-   Various output formats, including BLAST pairwise, tabular and XML,
16    as well as taxonomic classification.
17
18[![Build](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml/badge.svg)](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml)
19[![Build Status](https://api.travis-ci.com/bbuchfink/diamond.svg?branch=master&status=passed)](https://travis-ci.com/github/bbuchfink/diamond)
20[![image](https://img.shields.io/github/downloads/bbuchfink/diamond/total)](https://github.com/bbuchfink/diamond/releases)
21[![image](https://anaconda.org/bioconda/diamond/badges/version.svg)](https://anaconda.org/bioconda/diamond)
22[![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)
23[![image](http://diamondsearch.org/cit.svg)](https://scholar.google.com/citations?user=kjPIF1cAAAAJ)
24
25Documentation
26=============
27The online documentation is located at the [GitHub Wiki](https://github.com/bbuchfink/diamond/wiki).
28
29Support
30=======
31Diamond is actively supported and developed software. Please use the [issue tracker](https://github.com/bbuchfink/diamond/issues) for malfunctions and the [GitHub discussions](https://github.com/bbuchfink/diamond/discussions) for questions, comments, feature requests, etc.
32
33About
34=====
35DIAMOND is currently developed by Benjamin Buchfink at the Drost lab, Max
36Planck Institute for Developmental Biology, Tübingen, Germany (since 2019).
37Its development was supported for one year by the German Federal Ministry
38for Economic Affairs and Energy through an EXIST grant in 2018-2019. It was
39developed independently by Benjamin Buchfink from 2016-2018. Its initial
40version was developed in 2013-2015 by Benjamin Buchfink at the Huson lab, University
41of Tübingen, Germany.
42
43\[[:email:Email](mailto:buchfink@gmail.com)\]
44\[[Twitter](https://twitter.com/bbuchfink)\] \[[Google
45Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\]
46\[[Drost lab](https://drostlab.com/)\]
47\[[MPI-EBIO](http://eb.tuebingen.mpg.de/)\]
48
49**When using the tool in published research, please cite:**
50
51-   Buchfink B, Reuter K, Drost HG, \"Sensitive protein alignments at tree-of-life
52    scale using DIAMOND\", *Nature Methods* **18**, 366–368 (2021).
53    [doi:10.1038/s41592-021-01101-x](https://doi.org/10.1038/s41592-021-01101-x)
54
55Further publications:
56
57-   Buchfink B, Xie C, Huson DH, \"Fast and sensitive protein alignment
58    using DIAMOND\", *Nature Methods* **12**, 59-60 (2015).
59    [doi:10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176)
60