README.md

norg-suite

This package contains two programs:

• norg-seq: finds organelle genome insertions in the nuclear genomes with local alignments between the organelle and the nuclear genomes.

• norg-age: estimates evolutionary ages of organelle insertions that have been defined by norg-seq, using phylogenetic trees and genome alignments.

Requirement

norg-suite requires the following environment to run:

1. Python 3.x

2. Third party tools

   • norg-seq needs:

     • tantan (repeat masking): http://www.cbrc.jp/tantan/
     • LAST (local alignments): http://last.cbrc.jp/

   • norg-age needs:

     • MAFFT (multiple alignments): http://mafft.cbrc.jp/alignment/software/
     • RAXML (phylogenetic trees) : http://sco.h-its.org/exelixis/software.html

To prepare the above tools easily, there is a shell script which downloads the newest versions of the tools automatically. Under "tools" directory, you can use the script like this:

chmod +x fetch.sh && ./fetch.sh -a

After fetching the tools, please compile them by following each software instruction.

Usage

Prease see "doc" directory for the details. There is two types of manual formats, html and txt. We recommend to view html version for getting more detailed descriptions of norg-suite.

Manuals enclosed "html" or "text" named:

• norg-suite general description: norg-suite.html (html only)
• norg-seq user's manual : norg-seq.html|txt (html, txt)
• norg-age user's manual : norg-age.html|txt (html, txt)