How to get phylogenetic tree from kraken or bracken output file?
有人讨论如何用kraken的结果做进化树，
尝试其中的一种方法，

Mike Lee's tool GToTree
It will take a list of NCBI accession IDs for each genome and create a phylogenetic tree out of them.

Github: https://github.com/AstrobioMike/GToTree

conda create -y -n gtotree -c conda-forge -c bioconda -c astrobiomike gtotree

# /hwfssz5/ST_HEALTH/P18Z10200N0423/hutongyuan/analysis/fish/Abundance_kraken2/kraken_report
# /hwfssz5/ST_HEALTH/P18Z10200N0423/hutongyuan/database/kraken2
conda activate gtotree
GToTree -a ncbi_accessions.txt -f fasta_files.txt -H Bacteria -D -j 4
GToTree -h
-----------------  EXAMPLE USAGE  -------------------
GToTree -a ncbi_accessions.txt -f fasta_files.txt -H Bacteria -D -j 4

[-a <file>] single-column file of NCBI assembly accessions
[-g <file>] single-column file with the paths to each GenBank file
[-f <file>] single-column file with the paths to each fasta file
[-A <file>] single-column file with the paths to each amino acid file