Phylogenetic profiling

On my wiki I have a short summary of phylogenetic profiling. The program MrBayes is used for Bayesian inference for phylogeny and can be used for inferring relationships using binary type data such as phylogenetic profiles. The input to MrBayes is a NEXUS file and here is the example I will use: #NEXUS begin data;...

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Saving disk space with Perl

Disk space is cheaper these days but here's one way of using less disk space by working directly with gzipped files. Here's a very straight forward example of Perl code that opens a gzipped file and outputs a gzipped file. And here's some other code that just counts the number of lines in a file,...

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From SRA to FASTQ for SOLiD data

Before I forget how to do this (again), and waste time scouring the web, I'll make it a post. The last time I checked, the SRA will not be continued, however, there still exists a large repository of data that one may wish to (re)analyse. And sometimes the sequencing data of interest was performed on...

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