#The codes were originated from Dr. Jennifer Wisecaver

#Modified date and author: 20181022 & Xing-Xing Shen

Workflow of HGT identification

Step 1: AI calculation

perl calculate_alien_index_pct.pl -c test.config

Step 2: Building tree:

mafft --thread 6 --auto $filename > ${gene}_aln.fasta

trimal -in ${gene}_aln.fasta -out ${gene}_aln_trimmed.fasta -automated1

iqtree-omp -nt 6 -st AA -s ${gene}_aln_trimmed.fasta -m TEST -mrate G4 -keep-ident -bb 1000 -pre ${gene}

Step 3: Midpoint root a phylogeny with R:

mytree <- read.tree("$filename")

midponit_mytree <- ladderize (midpoint(mytree))

write.tree (midponit_mytree, "${gene}midpoint.tree")

Toy data (see compressed file "2_HGTs.zip") can be found on the figshare: https://figshare.com/articles/dataset/Tempo_and_mode_of_genome_evolution_in_the_budding_yeast_subphylum/5854692

For questions, please contact xingxingshen@zju.edu.cn

When using the pipeline in published research, please cite:

Shen X.-X., Opulente D.A., Kominek J.#, Zhou X., Steenwyk J., Buh K.V., Haase M., Wisecaver J.H., Wang M., Doering D.T., Boudouris J., Schneider R., Langdon Q.K., Ohkuma M., Endoh R., Takashima M., Manabe R., Čadež N., Libkind D., Rosa C., DeVirgilio J., Hulfachor A., Groenewald M., Kurtzman C.P., Hittinger C.T., Rokas A. 2018. The tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-1545. doi:10.1016/j.cell.2018.10.023