---
# System prepended metadata

title: Making simple tree for summary figure
tags: [prions-fo-life]

---

---
tags: prions-fo-life
title: Making simple tree for summary figure
---

# Making simple tree for summary figure

[toc]

## Targets
Tom noted these are the ones with confirmed prions we want to highlight. Manually getting NCBI assembly accessions to be able to tree with GToTree (turns out just took the first one for each, all had RefSeq versions except human):


| Target tax | Accession selected |
|------------|-----------|
| Saccharomyces cerevisiae | GCF_000146045.2 |
| Schizosaccharomyces pombe | GCF_000002945.1 |
| Podospora anserina | GCF_000226545.1 |
| Plasmodium falciparum | GCF_000002765.5 |
| Mus musculus | GCF_000001635.27 |
| Xenopus laevis | GCF_017654675.1 |
| Homo sapiens | GCA_000001405.29 |
| Drosophila melanogaster | GCF_000001215.4 |
| Arabidopsis thaliana | GCF_000001735.4 |
| Clostridium botulinum | GCF_000063585.1 |
| Campylobacter hominis | GCF_000017585.1 |
| *Methanobacteriales | GCF_000016525.1 |
| *Sulfolobales | GCF_019175345.1 |
| *Desulfurococcales | GCF_000017945.1 |
| **Bacteriophage |  |
| **Eukaryotic virus |  |

> \* I asked for more specific ones than these levels
> \** we can't include viruses on the tree, will just have to add them separately

## GToTree
This is going to be poor, but will enable a schematic, maybe we should overlay our cartoon onto a full tree or something.

### Conda env
```bash
mamba create -n gtotree -c conda-forge -c bioconda -c defaults -c astrobiomike gtotree=1.6.33

conda activate gtotree
```
### Code
```bash
# making list for GToTree 
printf "GCF_000146045.2
GCF_000002945.1
GCF_000226545.1
GCF_000002765.5
GCF_000001635.27
GCF_017654675.1
GCA_000001405.29
GCF_000001215.4
GCF_000001735.4
GCF_000063585.1
GCF_000017585.1
GCF_000016525.1
GCF_019175345.1
GCF_000017945.1
" > target-accs.txt
```

```bash
# making tree
GToTree -a target-accs.txt -H Universal -t -j 4 -o small-tree-for-cartoon-gtotree-out -F -B -G 0.4
```

