Timed MAFFT Alignment

This test performs an alignment of 100 pyruvate decarboxylase sequences.

Learn more about this test at the upstream project site: http://align.bmr.kyushu-u.ac.jp/mafft/software/.

This scientific test profile is maintained by Andrew Schofield. This OpenBenchmarking.org test profile was created on 6 December 2010 and last updated on 26 September 2020. To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark mafft.

This test has an average install time of 1 second and an average run-time of 2 minutes, 27 seconds.

200k+ Downloads + 10k+ Public Benchmark Results

Installation StatsTest Completion StatsOpenBenchmarking.orgEventsTimed MAFFT Alignment Popularitypts/mafft2015.102015.122016.022016.042016.062016.082016.102016.122017.022017.042017.062017.082017.102017.122018.022018.042018.062018.082018.102018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.08338281623241832134008

* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting.

Revision History

pts/mafft-1.6.1   [View Source]   26 Sep 2020 16:35 EDT
Tighten arguments of update over noise.

pts/mafft-1.6.0   [View Source]   26 Sep 2020 15:16 EDT
Update to newest MAFFT upstream 7.471 to address build issues with newer distros. Also use larger dataset input so it takes longer to run on modern hardware.

pts/mafft-1.5.0   [View Source]   04 Mar 2018 12:47 EST
Update against MAFFT 7.392, add Windows support.

pts/mafft-1.4.2   [View Source]   06 Feb 2018 19:40 EST
Minor cleanup to the install.sh

pts/mafft-1.4.1   [View Source]   06 Feb 2018 17:59 EST
Update download mirrors

pts/mafft-1.4.0   [View Source]   21 Feb 2012 10:36 EST
Support multi-threaded MAFFT build.

pts/mafft-1.3.0   [View Source]   07 Dec 2011 12:40 EST
Update against MAFFT upstream 6.864.

pts/mafft-1.2.0   [View Source]   06 Dec 2010 14:55 EST
Initial import into OpenBenchmarking.org

Suites Using This Test

C/C++ Compiler Tests

CPU Massive

Scientific Computing

Bioinformatics

Performance Metrics

Analyze Test Configuration:

Timed MAFFT Alignment 7.471

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.org metrics for this test profile configuration based on 240 public samples since 26 September 2020 with the latest data as of 28 October 2020.

Below is an overview of the generalized performance for components where there is sufficient statistically significant data based upon user-uploaded results. It is important to keep in mind particularly in the Linux/open-source space there can be vastly different OS configurations, with this overview intended to offer just general guidance as to the performance expectations.

Component
Percentile Rank
Seconds (Average)
Mid-Tier
75th
> 10
Median
50th
12
Low-Tier
25th
> 14
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA240 Results Range From 6 To 220 Seconds621365166819611112614115617118620121623150100150200250

Based on OpenBenchmarking.org data, the selected test / test configuration (Timed MAFFT Alignment 7.471 - Multiple Sequence Alignment - LSU RNA) has an average run-time of 2 minutes. By default this test profile is set to run at least 3 times but may increase if the standard deviation exceeds pre-defined defaults or other calculations deem additional runs necessary for greater statistical accuracy of the result.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkMultiple Sequence Alignment - LSU RNARun-Time3691215Min: 1 / Avg: 1.26 / Max: 10

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsMultiple Sequence Alignment - LSU RNADeviation3691215Min: 0 / Avg: 1.02 / Max: 9

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User Comments

Internal Server Error 500

http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2 returns Error 500 Internal server error

Post by honiix on 25 September 2017, 11.05.

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