<commit_before># A simple version for tree building

# Architecture
## Similarity Calculation
input: smile
output: distance matrix

## Preparing input for RapidNJ
input: distance matrix
output: RapidNJ input ([PHYLIP format](http://www.mothur.org/wiki/Phylip-formatted_distance_matrix))

## Run RapidNJ
input: filename for RapidNJ input<commit_msg>basic workflow<commit_after># A simple version for tree building

# Architecture
## Similarity Calculation
input: smile
output: distance matrix

## Preparing input for RapidNJ
input: distance matrix
output: RapidNJ input ([PHYLIP format](http://www.mothur.org/wiki/Phylip-formatted_distance_matrix))

## Run RapidNJ
input: filename for RapidNJ input
output: newick tree format

## Newick to Dot
input: newick file
output: dot file

## run graphviz on dot
input: dot filename
output: dot filename

## convert dot file to json with combination of other info
input: dot filename, other info
output: json
{'fraction_non_alphanumeric': 0.07805907172995781, 'fraction_numerical': 0.0, 'mean_word_length': 5.683098591549296, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6916480', 'n_tokens_mistral': 291, 'n_tokens_neox': 272, 'n_words': 108}