Software & Scripts
The Santos Lab maintains a GitHub repository as well as an OpenSuse Build Service (OBS) repository of scripts and software packages for population genetics, phylogenetics, phylogenomics, bioinformatics and next-generation sequencing (NGS). In the latter case, these are "rolled" as RPMs for CentOS 6 (these also work with Scientific Linux 6 [which we prefer] and other RHEL 6 clones). Consult the documentation of your particular EL6 Linux distribution for instructions on how to add additional software repositories to your system.
Examples from The Santos Lab on computational approaches and other CLI "tricks" are posted to Scott's Asciinema page, so also have a look to see what might be the latest there.
We also offer copies of various shell and perl scripts as well as software binaries related to biocomputing. Most of these should work on any UNIX/Linux operating system; however, some require a current version/installation of the Bioperl modules and/or are specific to Apple OSX with Intel hardware. Although some of these scripts have been written by members of the laboratory, many originate from the Stothard Research Group at the University of Alberta and the Advanced Center for Genome Technology at the University of Oklahoma. Another useful source for bioSoftware & Scripts is the "Tools" tab at the Natural Environment Research Council Environmental Bioinformatics Centre website. To download a script, right-click on the link and select "Download linked file as...". Please read the comments in the scripts for additional information on their usage.