xiekunwhy/vcf2tree

construct NJ-tree from vcf file

vcf2tree

construct NJ-tree from vcf file

Dependences

perl https://www.perl.org

R with ape package installed

plink2 https://www.cog-genomics.org/plink/2.0

parafly https://github.com/ParaFly/ParaFly

goalign https://github.com/evolbioinfo/goalign

gotree https://github.com/evolbioinfo/gotree

fastme http://www.atgc-montpellier.fr/fastme/binaries.php

All above can be intalled via conda or mambaforge, mambaforge(https://github.com/conda-forge/miniforge, choose Latest installers with Mamba in the base environment:) is recommended for China mainland users.

example

perl vcf2tree.pl -v Xian.vcf.gz -o vcf2tree -k snp -r F -c software.config.txt

than run q01 to q04 step by step, please parallize q02 to speed up the pipeline.

Change parameters and software path in software.config.txt according to your environment.