progressiveMauve

Mauve (genome alignment)

• Author: Dreycey Albin
• Date: 05/10/2019
• Updates: NAME (DATE): update descr; NAME (DATE): update descr,
• Program for genome alignment
• documentation (website): progressive mauve
• documentation (publication): URL TO PUBLICATION
• documentation (directions for using Mauve from the command line): progressiveMauve command line Directions

Installation

• installation for MacOS

wget http://darlinglab.org/mauve/snapshots/2015/2015-02-25/MacOS/Mauve-snapshot_2015-02-25.dmg;

• installation for Linux

wget http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64/mauve_linux_snapshot_2015-02-13.tar.gz;
tar -zxvf mauve_linux_snapshot_2015-02-13.tar.gz

Basic commands

INPUT

• using 3 genomes extracted from EvolSim into fasta format using the gbk_to_fna python script:

./linux-x64/progressiveMauve --output=threeway.xmfa --output-guide-tree=threeway.tree --backbone-output=threeway.backbone 001dreyceysim_1000.fna 039dreyceysimS040_269.fna 039dreyceysimX_373.fn

OUTPUT

001dreyceysim_1000.fna.sslist 
039dreyceysimX_373.fna.sslist
039dreyceysimS040_269.fna.sslist
threeway.backbone  
threeway.tree  
threeway.xmfa  
threeway.xmfa.bbcols```

Example_1

Input files

--> 3 genomes of interest

commands

• using 3 genomes extracted from EvolSim into fasta format using the gbk_to_fna python script:

./linux-x64/progressiveMauve --output=threeway.xmfa --output-guide-tree=threeway.tree --backbone-output=threeway.backbone 001dreyceysim_1000.fna 039dreyceysimS040_269.fna 039dreyceysimX_373.fn

Output files

• Output for this particular command

001dreyceysim_1000.fna.sslist 
039dreyceysimX_373.fna.sslist
039dreyceysimS040_269.fna.sslist
threeway.backbone  
threeway.tree  
threeway.xmfa  
threeway.xmfa.bbcols