Each directory within the phylogenies subdirectory MUST contain the following:
taxa.csv -- a csv file linking the taxon labels in
summary.treesto their correct glottocodes and xd_ids and society ids:
taxon glottocode xd_ids soc_ids
summary.trees -- a single summary tree in nexus tree format.
And may contain other files including:
original/ -- a directory storing the original tree files. Note: For programmatically created phylogenies like the ones from Glottolog, this directory is not present.
posterior.trees -- a posterior probability distribution of the trees (if available) in nexus tree format.
Makefile -- a
Makefileto generate summary.trees and posterior.trees from the original data.
If you want to run the Makefiles yourself then you will need to install the python-nexus library for the nexus_treemanip.py program.
Notes on adding a new tree:
- the directory name should reflect the source of the tree (e.g. gray_et_al2009) rather than the language family (e.g. austronesian.trees) as we might have multiple trees for the same language family, or trees that span families.
- the directory should be lower case.
- each directory must be added to index.csv