<p>The <a href="https://github.com/bbuchfink/diamond" rel="nofollow noreferrer">Diamond protein aligner</a> is a very popular tool for pairwise protein alignment which is much faster than blastp while having comparable sensitivity. Diamond also supports the use of using multiple compute nodes (similar to mpiBLAST). You can view the details of the new Diamond 2.0 release in <a href="https://www.nature.com/articles/s41592-021-01101-x" rel="nofollow noreferrer">this</a> recent Nature Methods paper (source of the image as well).</p>
<blockquote>
<p>...we aligned all 281 million protein sequences from the NCBI nr database against the UniRef50 database, which consists of 39 million sequences, using DIAMOND (v2.0.7) in ultra-sensitive mode...</p>
</blockquote>
<p><a href="https://i.sstatic.net/73rdB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/73rdB.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2021-09-15T01:06:17.697Z
Throckmorton thanks a lot for the suggestion! I'll have a look at this aligner now.
Johnny Tam
CC BY-SA 4.0
2021-09-14T19:34:05.993Z
2021-09-14T19:34:05.993Z
Throckmorton
<p>I am looking for a sequence alignment software capable of pairwise alignment of a large number of protein sequences (10^7).</p>
<p>I tried to go for mpiblast: <a href="https://wiki.canterbury.ac.nz/display/UCHPC/Installing+mpiBLAST" rel="nofollow noreferrer">https://wiki.canterbury.ac.nz/display/UCHPC/Installing+mpiBLAST</a></p>
<p>but seems their website was down.</p>
<p>Do you know any alternatives to mpiblast which is also highly efficient in protein sequence alignment?</p>
<p>Thanks!</p>

<phylogenetics><blast>
mpiblast alternatives?
# mpiblast alternatives?

(Asked by: username_0 on 2021-09-14)

I am looking for a sequence alignment software capable of pairwise alignment of a large number of protein sequences (10^7).

I tried to go for mpiblast: <https://wiki.canterbury.ac.nz/display/UCHPC/Installing+mpiBLAST>

but seems their website was down.

Do you know any alternatives to mpiblast which is also highly efficient in protein sequence alignment?

Thanks!

**Tags:** phylogenetics, blast

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## 1 answers

### Answer by username_1 on 2021-09-14. Score: 4 | Accepted answer

The [Diamond protein aligner](https://github.com/bbuchfink/diamond) is a very popular tool for pairwise protein alignment which is much faster than blastp while having comparable sensitivity. Diamond also supports the use of using multiple compute nodes (similar to mpiBLAST). You can view the details of the new Diamond 2.0 release in [this](https://www.nature.com/articles/s41592-021-01101-x) recent Nature Methods paper (source of the image as well).

> ...we aligned all 281 million protein sequences from the NCBI nr database against the UniRef50 database, which consists of 39 million sequences, using DIAMOND (v2.0.7) in ultra-sensitive mode...

[![enter image description here](https://i.sstatic.net/73rdB.png)](https://i.sstatic.net/73rdB.png)

> **Comments:**
> **username_0**: Throckmorton thanks a lot for the suggestion! I'll have a look at this aligner now.  

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