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martin-steinegger committed Jul 8, 2018
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@@ -3,7 +3,13 @@ MMseqs2 (Many-against-Many sequence searching) is a software suite to search and
The MMseqs2 user guide is available as [Github Wiki](https://github.com/soedinglab/mmseqs2/wiki) or as [PDF file](https://mmseqs.com/latest/userguide.pdf) (Thanks to [pandoc](https://github.com/jgm/pandoc)!)
Please cite: [Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/nbt.3988 (2017)](https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3988.html).
Please cite:
[Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/nbt.3988 (2017)](https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3988.html).
[Steinegger M and Soeding J. Clustering huge protein sequence sets in linear time. Nature Communications, doi: 10.1038/s41467-018-04964-5 (2018)](https://www.nature.com/articles/s41467-018-04964-5).
![alt tag](https://codeship.com/projects/58db4570-5f19-0134-0f23-2e28d2b4319e/status?branch=master)
![alt tag](https://ci.appveyor.com/api/projects/status/lq8nxeb0j8v38d1a?svg=true)
@@ -16,18 +22,12 @@ Please cite: [Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequ
## News
Keep posted about MMseqs2/Linclust updates by following Martin on [twitter](https://twitter.com/thesteinegger).
05/01/2018 New version of Linclust manuscript uploadd to bioRxiv: [Steinegger M and Soeding J. Clustering huge protein sequence sets in linear time. bioRxiv (2018)](https://doi.org/10.1101/104034). The combined MMseqs2/Linclust workflow (now the default when calling "mmseqs cluster" combines extreme speed and linear time complexity with BLAST-like sensitivity.
07/07/2018 Linclust has just been published at [Nature Communications](https://www.nature.com/articles/s41467-018-04964-5).
17/10/2017 MMseqs2 has just been published at [Nature Biotechnology](https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3988.html).
05/25/2017 We updated the Linclust manuscript. Linclust is now 3x faster and we added a metagenomic protein assembly application. Happy towel day. A pre-print can be downloaded here: [Steinegger M and Soeding J. Linclust: clustering billions of protein sequences per day on a single server (2017)](http://biorxiv.org/content/early/2017/05/25/104034).
30/01/2017 We added a new clustering workflow called "Linclust". Linclust can cluster sequences in linear time down to 50% sequence identity. The Metaclust95 and Metaclust50 database can be download at [metaclust.mmseqs.com](https://metaclust.mmseqs.com/). A preprint can be downloaded here: [Steinegger M and Soeding J. Linclust: clustering protein sequences in linear time (2017)](http://www.biorxiv.org/content/early/2017/01/29/104034.article-metrics).
19/12/2016 MMseqs2 has a mascot now. It is the "little Marv" and was lovingly crafted by Yuna Kwon. Thank you so much.
07/12/2016 We added a new parameter called --max-accept. This parameter limits the amount of alignments that get accepted. Please do not use --max-seqs to limit your result size since it decreases the sensitivity of MMseqs2.
## Installation
MMseqs can be installed by compiling the binary from source, download a statically compiled version, using [Homebrew](https://github.com/Homebrew/brew) or [Docker](https://github.com/moby/moby). MMseqs2 requires a 64-bit system (check with `uname -a | grep x86_64`) with at least the SSE4.1 instruction set (check by executing `cat /proc/cpuinfo | grep sse4_1` on Linux and `sysctl -a | grep machdep.cpu.features | grep SSE4.1` on MacOS).

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