Difference between revisions of "Asaq"
(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|Asaq}} |{{#vardefine:url|https://github.com/marinagarrote/ASAQ-method}} <!--CONFIGURATION: OPTIONAL (|...") |
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Alignment]][[Category:Sequencing]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|Asaq}} | |{{#vardefine:app|Asaq}} | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | The ASAQ method has been implemented in C++ to be run in a UNIX terminal. Given an alignment of four sequences, ASAQ computes three weights, one for each possible tree topology. | + | The ASAQ method has been implemented in C++ to be run in a UNIX terminal. Given an alignment of four sequences, ASAQ computes three weights, one for each possible tree topology. To run ASAQ it is necessary to have installed the C++ linear algebra library Armadillo |
<!--Modules--> | <!--Modules--> | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
<!--Citation--> | <!--Citation--> | ||
| − | {{#if: {{#var: citation}}|==Citation== | + | {{#if: {{#var: citation}}1|==Citation== |
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | Please cite the following papers if you use Armadillo in your research and/or software. | |
| + | Citations are useful for the continued development and maintenance of the library. | ||
| + | |||
| + | Conrad Sanderson and Ryan Curtin. [http://arma.sourceforge.net/armadillo_joss_2016.pdf Armadillo: a template-based C++ library for linear algebra]. Journal of Open Source Software, Vol. 1, pp. 26, 2016. | ||
| + | |||
| + | Conrad Sanderson and Ryan Curtin. [http://arma.sourceforge.net/armadillo_lncs_2018.pdf A User-Friendly Hybrid Sparse Matrix Class in C++]. Lecture Notes in Computer Science (LNCS), Vol. 10931, pp. 422-430, 2018. | ||
|}} | |}} | ||
Latest revision as of 15:10, 1 June 2022
Description
The ASAQ method has been implemented in C++ to be run in a UNIX terminal. Given an alignment of four sequences, ASAQ computes three weights, one for each possible tree topology. To run ASAQ it is necessary to have installed the C++ linear algebra library Armadillo
Environment Modules
Run module spider Asaq to find out what environment modules are available for this application.
System Variables
- HPC_ASAQ_DIR - installation directory
- HPC_ASAQ_BIN - executable directory
- HPC_ASAQ_LIB - library directory
Citation
If you publish research that uses Asaq you have to cite it as follows:
Please cite the following papers if you use Armadillo in your research and/or software. Citations are useful for the continued development and maintenance of the library.
Conrad Sanderson and Ryan Curtin. Armadillo: a template-based C++ library for linear algebra. Journal of Open Source Software, Vol. 1, pp. 26, 2016.
Conrad Sanderson and Ryan Curtin. A User-Friendly Hybrid Sparse Matrix Class in C++. Lecture Notes in Computer Science (LNCS), Vol. 10931, pp. 422-430, 2018.