Slackware and 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 system, almost exclusively from the scripts at With this post, I would like to give my sincere thanks to Slackware and the community.
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Converting sequences by squizz

Sometimes I need to have a DNA or amino acid sequence (or an alignment) in several different formats. A neat little program that can convert between different sequence formats is squizz. Its primary function is to serve as a sequence format file checker, but can do some conversions. Read the rest of this entry »

Geneconv: detect gene conversion

Geneconv is a program for detecting gene conversion between aligned DNA sequences. It can also search for gene conversion fragments from outside the alignment. The output results are ranked by P-values and presented in a spreadsheet manner. The data are valuable for bioinformatics studies and papers that deal with evolution.
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ALINE: colouring, numbering and annotation

Aline is an extensible WYSIWYG protein sequence alignment editor for publication quality figures. It canĀ  read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Read the rest of this entry »

Protein MSA secondary structure

I needed to predict the secondary structure of amino acid sequences, already in a multiple sequence alignment (MSA). This means that the sequences had gaps, which could be a problem. I searched the net for a suitable, easy-to-use application or online server. Read the rest of this entry »