mrnoutahi Some thoughts on boring stuff, and bioinformatics


Ukkonen’s Algorithm for generalized suffix tree in javascript, using d3js for visualization : SuffixTreeJS

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Why you should use ete for tree exploration and visualisation in python !

If you work with trees (phylogenetics or not) and you regularly use python, you have probably used or heard about one of the following packages: Bio.phylo, dendropy or ETE.

While each one of those packages has its own unique strengths and weaknesses, I particularly like the ETE module. Here is why !

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Fisher's Exact test for mxn contingency table

I was working on a project where I needed to compare categorical data in order to determine if there is any association between them. For my particular problem, a chi2 test wouldn’t work, so I needed a Fisher’s exact test. Since there aren’t any code in python to perform the Fisher’s exact test for larger than 2x2 table, I decided to write my own. You can find it here : FisherExact.

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First Post

2016 is near, and like any new year it comes with taking new resolutions.

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