SNPhylo: Difference between revisions
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Phylogenetic tree is a good tool to infer evolutionary relationships among various organisms so the tree has been used in many evolutionary studies. Consequently, phylogenetic tree based on SNP data have been determined in resequencing projects. However, there was no simple way to determine phylogenetic tree with the huge number of variants determined from resequencing data. Thus, we had developed new pipeline, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data. | Phylogenetic tree is a good tool to infer evolutionary relationships among various organisms so the tree has been used in many evolutionary studies. Consequently, phylogenetic tree based on SNP data have been determined in resequencing projects. However, there was no simple way to determine phylogenetic tree with the huge number of variants determined from resequencing data. Thus, we had developed new pipeline, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data. | ||
<!--Modules--> | <!--Modules--> | ||
== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
< | |||
==System Variables== | ==System Variables== | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 17:48, 10 June 2022
Description
Phylogenetic tree is a good tool to infer evolutionary relationships among various organisms so the tree has been used in many evolutionary studies. Consequently, phylogenetic tree based on SNP data have been determined in resequencing projects. However, there was no simple way to determine phylogenetic tree with the huge number of variants determined from resequencing data. Thus, we had developed new pipeline, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data.
Environment Modules
Run module spider snphylo to find out what environment modules are available for this application.
System Variables
- HPC_SNPHYLO_DIR - installation directory
Citation
If you publish research that uses snphylo you have to cite it as follows:
Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15(1).