Useful free software

Below is a variety of software that I use, but may never cite in a publication. Here is where they get their credit:

Basic document tools (i.e. de-crippling Windows)

Notepad++ (ideal for reading Linux files on Windows machines, or looking at large files)
7Zip (compression utility)
PuTTY, WinSCP (network utilities; see these tips for customizing Putty). Attempts to find alternatives with more polished GUIs have led to nothing but frustration (e.g. Open Text HostExplorer corrupted my OS).

Sequence analysis

Tablet (short-read alignment viewer)
Jalview, UGene ,BioEdit  (Sequence alignment)
FigTree (Phylogeny display)
DNA Master (all-purpose)

Population Modeling tools:

Henry Schaffer has written some programs:

– With Full Genetic construction of each
– With Emphasis on the pattern of heterozygosity over

Inbreeding – Full Sib Lines <>

Populus developed by Don Alstad and colleagues at the University of Minnesota particularly suitable for Biology
Undergrads or have background in Biology.

Programming tools:

Interactive tools:


Program writing:

Eclipse (a Java-centric IDE)

BioPerl,BioPython (libraries for common biological analyses)

See “programming for non-programmers” on my Cool Sciency Links page.

Operating systems:

Virtual Box (Virtual machine; allows installation of an OS inside of an OS)
CentOS (a reliable, but limited, Linux distribution; good for servers)
Fedora. Good for desktops. Not as polished as Mac or Win, but good enough. Frankly, I don’t think it’s any harder to learn than windows. It’s strength is that it’s internal workings are designed to be understandable for amatuers. The GPL ecosystem is much easier to navigate than proprietary software ecosystems (by which I mean that when someone tells you “here’s the solution to your problem”, it is easier to implement it in Linux than it is for proprietary systems, even if you are willing to throw money at the problem.)
Thoughts on Windows 8: great for tablets. The voice recognition utility is the only thing that makes it worthwhile for me (as long as I have access to MS Office).
Thoughts on MacOS (and iOS): I don’t see the point. I thought it could be an all-purpose system for me, but it turned out to have the worst of all worlds. The fanboyism and Mac jargon in their documentation interferes with actually finding solutions to problems.