PhyloStar / AutoCogPhylo

Repository for testing how good Bayesian phylogenetic algorithms fare with automated vs gold cognate judgments

AutoCogPhylo

Repository for testing how good Bayesian phylogenetic algorithms fare with automated vs gold cognate judgments

Requirements

• lingpy >= 2.6.1

Preparing the Data

To prepare the data, we offer further instructions in the file data.md, where you can find more information on how we cleaned and converted the data to our formats.

Preparing the LingPy-Analyses

LingPy analyses were created using four separate scripts:

• turchin.py: computes the turchin (consonant-class matching approach) analysis (see Turchin et al. 2010)
• sca.py: computes the cognates based on SCA distances (List 2012)
• edit-dist.py: computes cognates based on (normalized) edit-distance (Levenshtein 1965)
• lexstat.py: computes the lexstat-infomap (List et al. 2017) distances

Generating nexus files

python3 online_pmi.py data/IELex-2016.tsv.asjp ielex_pmi

python3 ldn_cluster.py data/IELex-2016.tsv.asjp ielex_ldn