# Bio::Phylo::CIPRES
Phylogenomic analysis on the CIPRES REST portal
## Prerequisites
Usage of CIPRES requires a
[DEVELOPER account](
https://www.phylo.org/restusers/register.action)
(not a normal user account) for the CIPRES REST API (CRA), and a
[registration](
https://www.phylo.org/restusers/createApplication!input.action) for the app
`corvid19_phylogeny`.With the account and app key, you can then populate a YAML file
`cipres_appinfo.yml` thusly, substituting the fields with pointy brackets with the
appropriate values:
```yaml
---
URL:
https://cipresrest.sdsc.edu/cipresrest/v1
KEY: <app key>
CRA_USER: <user>
PASSWORD: <pass>
```
Additional prerequisites, which should be resolved automatically during your chosen
installation procedure (conda, cpanm) are listed under the `PREREQ_PM` field in the file
[Makefile.PL](Makefile.PL).
## Installation
### CPANM
```bash
$ cpanm Bio::Phylo::CIPRES
```
## Example workflow
### 1. Aligning sequences
To align sequences in a FASTA file with
[MAFFT](
http://www.phylo.org/index.php/rest/mafft_xsede.html):
```bash
cipresrun \
-t MAFFT_XSEDE \
-p vparam.anysymbol_=1 \
-i <infile> \
-y cipres_appinfo.yml \
-o output.mafft=/path/to/outfile.fasta
```
- By adding the `-v` (or `--verbose`) flag, the XML returned by the server is shown. In
the last status check, this will show additional values for `-o`, e.g. to retrieve
STDERR and other outputs.
- Most other parameters shown on the REST documentation page can also be used.
- The output is written to a file with the same name is the output field (i.e. in this
case a file called `output.mafft`), which optionally ends up in a `-wd` working
directory.
### 2. Inferring trees
To infer trees from an aligned FASTA file using
[IQTree](
http://www.phylo.org/index.php/rest/iqtree_xsede.html):
```bash
cipresrun \
-t IQTREE_XSEDE \
-p vparam.specify_runtype_=2 \
-p vparam.specify_dnamodel_=HKY \
-p vparam.bootstrap_type_=bb \
-p vparam.use_bnni_=1 \
-p vparam.num_bootreps_=1000 \
-p vparam.specify_numparts_=1 \
-i /path/to/outfile.fasta \
-y cipres_appinfo.yml \
-o output.contree=/path/to/tree.dnd
```
