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sean-bam / Bioinformagick

Scripts for bioinformagicking
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Some questions about tree #1

Open ZongzhiWu opened 3 years ago

ZongzhiWu commented 3 years ago

Hi, sean! Recently, I read your article 'Thousands of previously unknown phages discovered in whole-community human gut metagenomes'. And I am very curious about the phylogeny method in the article and tried to replicate the method of the phylogenetic tree. Could you please provide the code of the phylogenetic tree of the paper? Thank you very much. If necessary, you can contact me by email zongzhiwu@stu.edu.pku.cn

ZongzhiWu commented 3 years ago

The common method of phylogenetic tree is to use trimmed MSA to build trees directly. I found that before you build final tree, you also use comparison of cluster to build a UGPMA. I guess the reason for this is that the TerL, mcp and portal is particularly distal due to making a huge tree of so many kinds of viruses?