Bio::Phylo::CIPRES

Phylogenomic analysis on the CIPRES REST portal

Prerequisites

Usage of CIPRES requires a DEVELOPER account (not a normal user account) for the CIPRES REST API (CRA), and a registration 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:

---
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.

Installation

CPANM

$ cpanm Bio::Phylo::CIPRES

Example workflow

1. Aligning sequences

To align sequences in a FASTA file with MAFFT:

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:

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