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Romulo Antao
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Phylip dependecies added to the project (OSX files)
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‎README.md

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#ncd_python
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How to use ncd.py
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"python ncd_calc.py data_folder compressor"
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"compressors available: zlib or bz2"
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"example: python ncd.py data/animals/ zlib"
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This program uses the Normalized Compression Distance to evaluate the similarity degree the mtDNA of different animals, thus inferring their genetic similarity.
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The results obtained from the ncd.py script are in the format required for post processing in Phylip (http://evolution.genetics.washington.edu/phylip.html).
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To generate a phylogenetic tree from the example dataset using the zlib compressor, the following procedure shall be followed:
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1) Execute the script
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python ncd.py data/animals/ zlib
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the output file, "q.phy" is a upper diagonal matrix
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2) execute the Phylip program neighbor
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./phylip-3.695/neighbor
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3) Choose "q.phy" as source and select Upper Triangular Data Matrix (R). Process the files and the program will output:
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Output written on file "outfile"
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Tree written on file "outtree"
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Done.
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3) Execute the script "name_replace" to introduce the names of the animals in the outtree file
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python "name_replace.py"
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4) Execute the Phylip program drawtree
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./phylip-3.695/neighbor
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5) Choose "outtree" as the input file and "font1" as the used font. Select option (B) to not use branch length and produce the output file.
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6) the result phylogenetic tree will be saved in the newly created "plotfile"

‎font1

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‎ncd.py

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from itertools import combinations
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file_datas = {}
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files = glob(glob_files+'*')
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for filec in files:
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file_datas[filec] = open(filec).read()
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