Skip to main content

Wrapper for the Phyluce phylogenomics software package

Project description

Tests codecov Quality Gate Status

UCEasy: a wrapper for the PHYLUCE software package

UCEasy is a wrapper to automate manual procedures of the PHYLUCE software package by abstracting the pipeline steps into 3 major commands and choosing sensible defaults for its command-line options, easing the execution and improving reproducibility.

At the moment, the only software package for analysing ultraconserved elements (UCEs) is PHYLUCE, but its execution can be quite challenging especially for non-computer experts. UCEasy is a convenient tool that automates the execution of common tasks for most types of UCE analysis, these being Quality Control, Assembly and UCE Processing.

Installation Guide

Dependencies

  • Python ^3.7
  • PHYLUCE ^1.6

See releases for pre-built binaries for Linux. Or install it from PyPI:

$ pip install uceasy

Then, make sure you have a working installation of PHYLUCE, check out the installation guide at PHYLUCE's documentation.

Workflow

The operations Quality Control, Assembly and Phylogenomics represent the following workflow.

The colored boxes are UCEasy CLI commands.

$ uceasy quality-control
$ uceasy assembly
$ uceasy phylogenomics

Explore the options for these commands with the --help flag. For a guide of how to use UCEasy see: Tutorial.

Acknowledgements

We thank the following institutions, which contributed to ensuring the success of our work:

Ministério da Ciência, Tecnologia, Inovação e Comunicação (MCTIC)

Museu Paraense Emílio Goeldi (MPEG)

Instituto Nacional de Pesquisas da Amazônia (INPA)

Centro Universitário do Estado do Pará (CESUPA)

Funding

This work has been supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (grants 149985/2018-5; 129954/2018-7).

Authors

Marcos Paulo Alves de Sousa Caio Vinícius Raposo Ribeiro Lucas Peres Oliveira Romina do Socorro da Silva Batista

Contact

Dr. Marcos Paulo Alves de Sousa (Project leader)

Email: msousa@museu-goeldi.br Laboratório de Biologia Molecular Museu Paraense Emílio Goeldi Av. Perimetral 1901. CEP 66077- 530. Belém, Pará, Brazil.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for uceasy, version 0.2.1
Filename, size File type Python version Upload date Hashes
Filename, size uceasy-0.2.1-py3-none-any.whl (10.6 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size uceasy-0.2.1.tar.gz (11.0 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page