Category Archives: Academic

Shorten contents of spreadsheet cells

I have a spreadsheet file with a list of species’ Latin names. I want to automatically create abbreviations for each species, by shortening both the genus and specific epithet to a certain number of characters. Here’s how to do it.

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Trimming trees with TreeBeST

I needed a program that can easily trim branches from a phylogenetic tree and came across TreeBeST (Tree Building guided by Species Tree). TreeBeST is a neat and versatile program that builds, manipulates and displays phylogenetic trees and seems to … Continue reading

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NCBI Edirect

I am preparing some scripts for the automated retrieval of biological sequences from NCBI. I wanted to find a way to easily download CDS (coding DNA sequence), amino acid sequences and so on. I googled a bit and it seems … Continue reading

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Slackware and SlackBuilds.org cited in a scientific publication

The latest paper from our research group has just been published in Scientific Reports. A big part of the work was done in silico, using different software tools and databases. All bioinformatics software used locally was installed on a Slackware64 … Continue reading

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Archaeopteryx configuration 2

Couple of years ago, I wrote about the configuration file of Archaeopteryx, a phylogenetic tree analysis program. I have set it to use native ui, as described in my old post. However, some things have changed meanwhile, so in order … Continue reading

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