How to analyze the population genetic Evolutionary Tree in R language
This article mainly explains "how to analyze the population genetic evolution tree in R language". Interested friends might as well take a look. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn "how to analyze the population genetic evolution tree in R language".
Population genetic evolution tree analysis method:
Cd $workdir # back to the working directory mkdir 01.phylo_treecd 01.phylo_tree# file format conversion run_pipeline.pl-Xmx5G-importGuess $workdir/00.filter/clean.vcf.gz\-ExportPlugin-saveAs supergene.phy-format Phylip_Inter# maximum likelihood method to construct evolutionary tree # method 1:fasttree construct evolutionary tree fasttree-nt-gtr supergene.phy > fasttree.nwk# method 2:iqtree construct evolutionary tree set boots value Maximum likelihood method iqtree2-s supergene.phy-st DNA-T 2-mem 8G\-m GTR-redo\-B 1000-bnni\-- prefix iqtree # method 3:raxml Construction Evolutionary Tree maximum likelihood method # raxml-ng-msa supergene.phy-model GTR-prefix raxml_tree\ #-threads 2-seed 1231 > raxml.log 2 > raxml.err## with bootstrap#raxml-ng-all-msa supergene .phy-- model GTR-- bs-trees 1000\ #-- prefix raxml_tree_bootstrap-- threads 2-- seed 1231 > raxml_bs.log 2 > raxml_bs.err# method Construction Evolutionary Tree Phylip format requires no more than 10 sample ID characters Otherwise, it will truncate cp supergene.phy infileecho-e "Y\ n" | dnadistcp infile.dist infileecho-e "Y\ n" | neighbormv outtree outtree.nwk so far, I believe you have a better understanding of "how to analyze population genetic evolution tree in R language". You might as well do it in practice! Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!
