1. Introduction to PGAP-X

Firstly, introduce myself...

1.1. What is PGAP-X

PGAP-X is a tool or so called "platform" for comparative genomics data analysis and viusalization, especially for procaryotic genomes. This tool integrates four functional modules including multi-sequence alignment("Genome Alignment"), orthologous gene identification("Orthologs Analysis"), genome variation analysis("Variation Analysis"), and pan-genome analysis("Pan-genome Analysis").

PGAP-X also provides visualizing components respectively for each functional module.

At the same time, PGAP-X accepts other comparative genomics analyzing results imported by users and provides corresponding visualization results with powerful compatibility.

The advantage of PGAP-X over traditional comparative genomic tools are that this tool is compatible for major operation systems(Windows and Linux), it can be deployed conveniently on researcher's personal computers; it is easy to operate and can provide intuitional visualization results; it intergrates multiple functional modules and can carry out a comprehensive comparative genomics analysis.

1.2. Suggestions with PGAP-X

PGAP-X is a strong and robust tool, you can use it in any way as you want, after all, you are its master. However, if you want to use it as expediently as possible, you may want to follow these suggestions bellow:

  • Read this user guider through and carefully
  • Check you file format of your data and folders in your workspace carefully
  • Use Windows platform
  • As we talked above, this tool is compatible for Linux, but we have more tests on windows platform, and we do not guarantee it has the same performance on linux.
  • Try any functinal buttons or signals you can use in the tool when analyzing.
  • 1.3. Developing environment

    PGAP-X is based on C++ programming language and Qt framework.