- User guide to MUSCLE with instructions on how to download. I used this to make the multiple alignments and phylogenetic trees.
- This website is useful for visualizing the alignments (muscle just spits out another fasta).
- Tools to make the phylogenetic trees: I used the Drawtree Java app.
- Roadmap Epigenomics Project metadata
Download from here. Bolded primates are infected by malaria.
| Scientific name | Common name |
|---|---|
| Aotus nancymaae | Nancy Ma's night monkey |
| Aotus trivirgatus | Night monkey |
| Callithrix jacchus | Common marmoset |
| Cebus capuchinus imitator | Capuchin monkey |
| Cercocebus atys | Sooty mangabey |
| Chlorocebus aethiops | Grivet |
| Galveopterus variegatus | Malayan flying lemur |
| Gorilla | Gorilla gorilla |
| Macaca fascularis | Crab eating macaque |
| Macaca mulatta | Rhesus macaque |
| Mandrillus leucophaeus | Drill |
| Nomascus leucogenys | Gibbon |
| Pan paniscus | Bonobo |
| Pan troglodytes | Chimpanzee |
| Papio anubis | Baboon (olive) |
| Pilicolorbus tephrosceles | Ugandan red colobus |
| Pongo alebii | Orangutan |
| Rhinopithecus roxellana | Golden snub-nosed monkey |
| Saimiri boliviensis | Squirrel monkey |
| ? | Bushbaby |
| ? | Denisova |
| ? | Green Monkey |
| ? | Marmoset |
| ? | Proboscis monkey |
| ? | Tarsier |