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tutorial.md

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This is a mini tutorial where we give examples on running each rooting method (Outgroup, Midpoint, MinVAR, Root-to-Tip) found in the use_cases folder.

If you installed FastRoot using PyPI (i.e. pip), download use_cases.zip to your machine and unzip it before trying the examples.

Outgroup Rooting

An example is given in the folder use_cases/OG. Starting from the base directory,

   cd use_cases/OG

Inside this folder you will find a list of input trees (input.trees), a list of outgroups (outgroups.txt), and two bash scripts to root these trees using Outgroup Rooting. One script defines the outgroups as a file (run_OG_file.sh) while the other defines them as a list (run_OG_list.sh). To root the input trees using this method, either run one of the scripts

   ./run_OG_file.sh

or call as follows:

   FastRoot.py -m OG -i input.trees -g outgroups.txt -o output.trees

Midpoint Rooting

An example is given in the folder use_cases/MP. Starting from the base directory,

   cd use_cases/MP

Inside this folder you will find a list of input trees (input.trees) and a bash script to root these trees using Midpoint Rooting (run_MP.sh). To root the input trees using this method, either run the script

   ./run_MP.sh

or call as follows:

   FastRoot.py -m MP -i input.trees -o output.trees

MinVAR Rooting

An example is given in the folder use_cases/MV. Starting from the base directory,

   cd use_cases/MV

Inside this folder you will find a list of input trees (input.trees) and a bash script to root these trees using MinVAR Rooting (run_MV.sh). To root the input trees using this method, either run the script

   ./run_MV.sh

or call as follows:

   FastRoot.py -m MV -i input.trees -o output.trees

Root-to-Tip Rooting

An example is given in the folder use_cases/RTT. Starting from the base directory,

   cd use_cases/RTT

Inside this folder you will find a list of input trees (input.trees), the sampling times (sampling_times.txt), and a bash script to root these trees using Root-to-Tip Rooting (run_RTT.sh). To root the input trees using this method, either run the script

   ./run_RTT.sh

or call as follows:

   FastRoot.py -m RTT -i input.trees -t sampling_times.txt -o output.trees