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#Introduction
PorthoMCL is a fast and easy to run tool for identifying orthology among any number of genomes with minimal requirements. PorthoMCL will facilitate comparative genomics analysis with increasing number of available genomes thanks to the rapidly evolving sequencing technologies.
The workflow of PorthoMCL is similar to that of OrthoMCL. However, instead of depending on an external database server, PorthoMCL uses a sparse file structure for more efficient data storage and retrieval.
PorthoMCL is much faster and scalable than OrthoMCL.
Please cite PorthoMCL's paper if you used it in your research:
PorthoMCL: Parallel orthology prediction using MCL for the realm of massive genome availability
Ehsan Tabari and Zhengchang Su
Big Data Analytics 2017 2:4 DOI: 10.1186/s41044-016-0019-8
#How to run
You can use the supplied [script](Run Fast) to run porthomcl on a single machine.
Or you can use the Detailed Manual to run steps as you wish.
We also have provided a template for Torque job schedulers.
Additionally you can use this [script](Download from Genbank) to retrieve protein sequences from Genbank.
There are very few requirements for PorthoMCL. Here are the list of the things needed to run PorthoMCL
- Perl 5.x
- Python 2.x
- NCBI Blast
- MCL
Perl and Python come preinstalled on most Linux and Unix (OS X). You need to install them on Windows.
This implementation removes the need for a database server. Therefore, you don't need to install DBI or DBD::mysql modules for your perl.