So there are a lot of programs out there that allow you to manually edit an alignment but few will have all of the features that I am after.
1. Must be able to switch easily between nucleotide and protein translation
2. Must be able to manually edit the alignment, including the ability to 'drag'
3. For free.
The best one I know of is Se-Al, but it no longer works for Mac, and was pretty buggy to begin with.
Second best is Mega but also super buggy on mac and doesn't have the crucial dragging feature.
BioEdit can be installed on a Mac with OS-X using WINE windows emulator:
http://phylogeneticgeek.wordpress.com/2011/08/05/how-to-install-bioedit-on-a-mac/
Or by installing a virtual windows machine using something like VMware.
Although it has a steep learning curve, ARB has a great aligner. It is based on Linux but can be run on a Mac. It can take a lot of effort to get it all up and running but it is a very powerful tool for aligning, managing large sequence databases and tree construction.
http://www.arb-home.de/
This is also a very helpful page on using ARB on Macs.
http://www.haloarchaea.com/resources/arb/
Best of luck!
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools