Home

Steps used to analyse PANGEA data from South Africa.

• South Africa
  • Step 1: Get South African sequences from PANGEA extract
  • Step 2: Get gag, pol and env from HIV genomic sequences
  • Step 3: Get only gene sequences >= 800 bp
  • Step 4: Subtype sequences per gene
  • Step 5: Download GenBank HIV sequences
  • Step 6: Get sequences from PANGEA
  • Step 7: Create FASTA database for blast
  • Step 8: Merge databases for blast
  • Step 9: blastn per gene
  • Step 10: Get 3 best matches
  • Step 11: Get metadata for best matches
    • For GenBank CGR sequences
    • For PANGEA CGR sequences
  • The case of env gene
  • Step 12: DNA sequence alignment
  • Step 13: Removal of drug resistance sites
  • Step 14: Detection of recombinant sequences
  • Step 15: Removal of additional CGR sequences
  • Step 16: Estimation of phylogenetic trees
  • Final DNA sequence alignment

South Africa

• Wait for ML runs to finish then run bash scripts. Read about scripts here.
• After running bash scripts, you should have the best ML tree. Remove the last 0,0 that RAxML add to the newick file. I remember that this would cause tree to show as rooted instead of unrooted.
• Run treedater on the best ML tree. You can use R scripts treedater_gag.R, treedater_pol.R, and treedater_env.R.

NOTE that scripts used for treedater analyses are organized in three sets per gene. For example: treedater_pol.R, pol.R and get_SA_data.R. You should run script treedater_pol.R only. The other two scripts are sourced inside this script or pol.R.

---

---

BASH SCRIPTS

Because I run the search for best maximum likelihood tree in parallel and using RAxML-NG, I wrote the bash scripts located here to pos-process all the files that are generated.

ML_script.sh is used to pos-process files generated when searching for the best maximum likelihood tree.

bootstrap_script.sh is used to pos-process files for the bootstrapped trees.

ALWAYS REMEMBER TO CHANGE IN SCRIPT THE DIRECTORY IN WHICH YOUR FILES ARE LOCATED

---

VERSION OF PROGRAMS I USED

MAFFT version 7.427 (2019/Mar/24)

RAxML-NG version 0.8.1

RDP4 version 4.97

AliView version 1.18.1

R version 3.5.1

BLAST command line applications version 2.6.0+

EDirect version 11.1