Post date: Jul 19, 2020 9:5:7 PM
Step 1 is to convert our data in XML format. This can be done using the BEAUTi program.
BEAUti can only handle nexus, fasta, and alignments in BEAST 1 and 2 xml format. (source: https://www.beast2.org/snapp-faq/)
I used the following script: https://raw.githubusercontent.com/BEAST2-Dev/SNAPP/master/script/vcf2nex.pl
to convert the vcf to nexus format file which is composed of binary information from the vcf fil (0/1).
There is a difference between BEAST and BEAST2 so I came back to BEAST because it seems better developed.
I am following this tutorial: https://beast.community/first_tutorial
The tutorial uses the following notions:
HKY model = 5-parameter DNA substitution model - transition rate, transversion rate that conserves the strong/weak properties of nucleotides, transversion rate that conserves the amino/keto properties of nucleotides, substitution rate and ?
gamma model of rate heterogeneity = model that takes into account variability of mutation sites accross sites. In the gamma case, the distribution follows a gamma distribution. One parameter describes it, aplha. When alpha is small, there is great heterogeneity accross sites with a few sites having a high mutation rate and a lot of sites nearly invariant. A big alpha describes a distribution with few heterogeneity between sites. (http://www.bioinf.man.ac.uk/resources/phase/manual/node81.html )
1 - Open BEAUTi
java -cp lib/launcher.jar beast.app.beauti.BeautiLauncher
BEAST can also import FASTA files (as long as the sequences have been aligned)
2 - Load nex file, or fasta
3 - Set up the taxa dates if they are relevant to the study - our samples can be considered as the tips for this study, they all are "0".
4 - problem with Java version