How can I construct a phylogenetic tree based on the SNP's shared between strains? I have whole genome SNP calls different strains in a multi-sample vcf. (raw fastq also)
Are there any tools that can take the vcf as an input for creating phylogenetic trees? Or do I need to convert the multi-sample vcf to another matrix? Which kind of matrix would that be how can I create it from the vcf?
Is there a list somewhere of popular packages that kan be used for creating phylogenetic trees? Or guides on how to go from a multi-sample vcf to a plylogenetic tree.
First of all, you may need to transform your vcf to FASTA/PHYLIP. This tool may help you: https://github.com/edgardomortiz/vcf2phylip
After you accomplish acquiring your FASTA/PHYLIP alignment file...
Do you have any sequence to root your analysis (or does any of those sequences is a root independent of your samples)?
In case the answer is yes, I may suggest making an exploratory analysis via PHYML: http://www.atgc-montpellier.fr/phyml/ utilizing the presents of all the features. If you want something more used in papers, go for RAxML. The CIPRES web server has the newer version (http://www.phylo.org/)
*With RAxML you should pre-analyze the alignments with jModelTest to determine the best fit model and/or with partitionFinder to see if the full sequence should be computed under the same substitution model.
In the case the answer is no, I suggest you the SPLITSTREE software. (http://www.splitstree.org/), it is very helpful to resolve phylogenetic relations between individuals inside the same group and it has various algorithms to construct different trees. Is super user-friendly.
Dear Abhijeet Singh
Yes, I just read your answers to the 2 questions. Thank you very much.
Yes, Phylogenetic trees need sequence information, So with the VCF and the reference sequence (fasta) I was able to recreate the sequence information for all my strain and use them to construct a phylogenetic tree.
Jose Alberto Lopez-Aleman Thank you
Yes, I am exploring PHYML at this moment and Phylo also.
Hi
May this VCF2PopTree can help you.
VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
Article VCF2PopTree : a client-side software to construct population...
By VCF file you can determine 'phyloP' scores, phyloP scores measure evolutionary conservation at individual alignment sites compared to the evolution that is expected under neutral drift.
A phylogenetic tree can be constructed directly from a VCF file. The simple software VCF2PopTree reads a VCF file and builds a tree in few minutes. It also produces pairwise distance matrix from a VCF file, which can then be used as an input file for the popular software such as MEGA.
Software: https://github.com/sansubs/vcf2pop
Paper: VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. PeerJ, Vol.7, e8213; 2019
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