Vcf2Tree is a pipline for make a evolutionary tree. It is the downstream analysis of GTAK4. Vcf2Tree is a tool to build a phylogenetic tree using SNP.vcf（or 4DTV.vcf）!
- sample.vcf (The length of the material name grouped in vcf must be <= 10 characters. Characters > 10 will be automatically truncated to 10 characters.) (if run 4DTV,the input.vcf must from snpEff!) input.vcf must vcf,vcf.gz is not support!
- output_prefix （Only characters can be used, not paths. if use like
./demo/50kordemo/50kwill be course a ERROR.） - genome.fa (only required when run
4DTv!)
Output file (all the output file will be put in run path!This version does not support defining output paths!)
- -viq ${output}.min4.phy.contree and ${ouput}.min4.phy.treefile
- -vdp ${output}.cons.vdp.tree
- -vp ${output}.nei.tree and ${output}.contree
- -vdf ${output}.vdf.tree
- 4DTv ${output}.4dtv.vcf
#get tree by iqtree (run fast，can auto choose the best suitable Model) Highly recommended!!!
Vcf2Tree -viq input.vcf output_prefix
Vcf2Tree --vcf2iqtree input.vcf output_prefix
#get tree by VCF2Dis and phylip (third fast)
Vcf2Tree -vdp input.vcf output_prefix
Vcf2Tree --vcf2Dis_phylip input.vcf output_prefix
#get tree by VCF2Dis and fastme (second fast,Inconsistent with the results constructed by other methods )
Vcf2Tree -vdf input.vcf output_prefix
Vcf2Tree --vcf2Dis_fastme input.vcf output_prefix
#get tree by phylip (slow！but accurate)
Vcf2Tree -vp input.vcf output_prefix
Vcf2Tree --vcf2phyliptree input.vcf output_prefix
# get 4DTV.vcf
Vcf2Tree 4DTv input.vcf output_prefix genome.fa
# get 4DTV.vcf and tree
Vcf2Tree 4DTv input.vcf output_prefix genome.fa -viq
Vcf2Tree 4DTv input.vcf output_prefix genome.fa -vdp
Vcf2Tree 4DTv input.vcf output_prefix genome.fa -vp
Vcf2Tree 4DTv input.vcf output_prefix genome.fa -vdf
demo:
Vcf2Tree -viq ${PWD}/demo/50k.vcf 50k
Vcf2Tree -vdp ${PWD}/demo/50k.vcf 50k
Vcf2Tree -vp ${PWD}/demo/50k.vcf 50k
Notes:
The output tree file can be visual by :
Figtree https://github.com/rambaut/figtree/releases (base Java)
ITOL https://itol.embl.de/upload.cgi(online)
ggtree https://github.com/YuLab-SMU/ggtree (R packages)
Python3 is required (make sure python3 has been install in your environment!)
The other require software have been put in this packages file.Just run bash Install.sh
bash Install.sh
source ~/.bashrc