Category: How to tutorials
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How to Locally Build and Test a Bioconda Program
Bioconda is a curated set of packages and programs useful in computational biology and bioinformatics. It’s similar to Anaconda, or more accurately, a channel of Conda, providing platform-independent bioinformatics related packages. I came to fully appreciate the Conda package manager for Python and R (and some other command-line tools) once I started heavily analyzing biological…
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Creating a Publication Quality Phylogeny Using ggtree
A decade ago, circa 2012-2013, I used MEGA5 to infer phylogeny using simple Neighbour-Joining methods, and used the figure generated by MEGA5 to present and publish my results. Later, when I started learning other phylogeny reconstruction methods like Maximum Likelihood (ML) and Bayesian (which does not draw the tree for you), I started to explore…
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Leveraging Power of Parallelization in UNIX Scripts
I needed to convert a bunch of bam files back into fastq files. I was implementing a regular for loop to load the files and convert them, one by one, serially. After running the first batch of conversion, I realized that the process is too slow, and is not the best thing to do when…
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Phylogeny from multi-locus sequences aka MLSA
For one of my Ph.D. projects, I had to generate phylogeny from multi-locus sequence data. Often I have to repeat similar analyses and need to go back to the previous workflow to check what I actually did. I’m sharing the protocol here mainly to help my future self, and may be this is useful to…
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Calculating Fst for haploid data in R
How to estimate the fixation index, FST, to test for population differentiation in R