pegi3s/rootdigger repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of Root Digger⁠, a program, that will, when given a multiple sequence alignment and an unrooted tree with branch lengths, place a root on the given tree.

To obtain the application help, you just need to run: docker run --rm pegi3s/rootdigger rd --help.

⁠Using the Root Digger image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/rootdigger rd --msa /data/sequences_aligned.fasta --tree /data/Newick_tree_file --mode

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTA file you want to align.
• sequences_aligned.fasta to the actual name of your aligned FASTA file.
• Newick_tree_file to the name of the Newick file containing the unrooted tree with branch lengths.
• --mode to either --exhaustive or --early-stop.