Protocols
My projects are in the area of comparative evolutionary genomics. Here I will share protocols developed or adopted by me for various purposes. Please feel free to contact me if you have questions, need help or something does not work.
Custom scripts supplied with the protocols are not guarantied to work. Here is the license statement [LICENSE].
Target capture sequencing data analysis and phylogenetics of Fragaria species
Three following protocols describe major steps employed in my paper with Noah Rosenberg, John Syring, and Aaron Liston on strawberries
(Kamneva et al. In revision).
Assembling haplotypes from NGS data for di- and polyploids
This is a long protocol which walks you through the process starting with NGS reads
for di- or polyploid species and eventually assembling haplotype sequences.
Phylogeny reconstruction using haplotype and consensus sequences from several Fragaria species
This is another long protocol which walks you through building gene trees from mixture of haplotype and consensus sequences
derived for about 20 species of Fragaria.
Demonstrates how to find and test hybridization event in species history using gene trees.