Difference between revisions of "PATHd8"
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(Created page with "Category:SoftwareCategory:biologyCategory:phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pathd8}} |{{#vardefine:url|http://www2.math.su.se/PATHd8...") |
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==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory | ||
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 22:11, 19 February 2018
Description
PATHd8 is implemented in the C-program PATHd8 and is freely available from this website. The program works instantaneously even for very large phylogenetic trees. (The time-complexity is O(n*t), where n is the number of nodes and t is the number of time contraints.)
Environment Modules
Run module spider pathd8 to find out what environment modules are available for this application.
System Variables
- HPC_{{#uppercase:pathd8}}_DIR - installation directory
- HPC_{{#uppercase:pathd8}}_BIN - executable directory
Citation
If you publish research that uses pathd8 you have to cite it as follows:
The program PATHd8 is based on the manuscript
- Estimating divergence times in large phylogenetic trees by Tom Britton, Cajsa Lisa Anderson, David Jacquet, Samuel Lundqvist and Kåre Bremer, in Systematic Biology 56:5, pp 741 - 752 .
- Britton, T., B. Oxelman, A. Vinnersten, and K. Bremer. 2002. Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution 24:58-65.