TreeMerge

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This repository contains scripts for generating pair-wise merged tree files and a new entry point to TreeMerge with additional input files.

Here is an overview of each script. For the full command line reference, you can also run the python files with the --help flag.

get_merge_list.py

This file is used to generate a minimum spanning tree as well as to generate a file which defines which pairs of trees must be merged together in order for TreeMerge to ingest them.

python get\_merge\_list.py --starting-tree <input tree> --output-prefix <output prefix> -- <space separated list of constraint trees>

setup_merger.py

This file is used to compute the induced starting trees needed for the pair-wise mergers

python setup\_merger.py --starting-tree <input tree> --files-needed <output named files_needed from get_merge_list.py> --output-prefix <output prefix> --merger-choice njmerge --guide-choide induced

run_merger.py

This file is used to run the pair-wise mergers and create pair-wise merged trees

python run\_merger.py --starting-tree <input tree> --files-needed <output named files_needed from get_merge_list.py> --output-prefix <output prefix> --merger-choice njmerge --guide-choice induced

treemerge.py

This file is the original treemerge that was modified to take in a predetermined minimum spanning tree. It expects the pair-wise trees to already have been computed on the input minimum spanning tree with ther branch lengths already estimated.

python treemerge.py -s <input tree> -m <input matrix> -x <input matrix taxon list> -o <output prefix> -p <paup binary> -w <working directory> --mst <minimum spannig tree> -t <space separated list of constrait trees>