You may already be familiar with my shameless love for the Geneious Pro software. My lab uses this software to view and annotate trace files, assemble contigs, and make alignments. For these purposes, Geneious is superior to Sequencher and available for only a fraction of the price ($249 for students/$495 for other academics). What's more, the folks at Geneious are constantly making improvements. Some really cool ones are making their debut in the latest beta release (v 4.6). My personal favorite is the automated assembly function, which can be used to automatically generate contigs from sequences that share some common motif in their file names (e.g., species1_forward & species1_reverse). We're using this function to put together forward and reverse reads from short DNA fragments. Another major shortcoming of Geneious bites the dust... Of course, there are still some bugs to be worked out (we are, for example, having problems automating end trimming and assembly of sets of sequences >40), but the folks at Geneious are actively working to solve these problems.
Thursday, March 19, 2009
The New Geneious Pro Beta (v4.6): A Sweet Upgrade
You may already be familiar with my shameless love for the Geneious Pro software. My lab uses this software to view and annotate trace files, assemble contigs, and make alignments. For these purposes, Geneious is superior to Sequencher and available for only a fraction of the price ($249 for students/$495 for other academics). What's more, the folks at Geneious are constantly making improvements. Some really cool ones are making their debut in the latest beta release (v 4.6). My personal favorite is the automated assembly function, which can be used to automatically generate contigs from sequences that share some common motif in their file names (e.g., species1_forward & species1_reverse). We're using this function to put together forward and reverse reads from short DNA fragments. Another major shortcoming of Geneious bites the dust... Of course, there are still some bugs to be worked out (we are, for example, having problems automating end trimming and assembly of sets of sequences >40), but the folks at Geneious are actively working to solve these problems.
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10 comments:
I just wanted to comment so I could add another Geneious link. I thought the five or six Geneious links that you added were not enough. Someone cannot stop adding Geneious links, it's quite contagious.
A classic anonymous comment, I love it. Does your thinking that I'm trying to load search engines underlie your sarcasm?
Man, sarcasm? No way. Just because I'm anonymous?
For a person that makes sequence alignment with Geneious, you're pretty clever, huh?
Ha, there you go another Geneious link, for you. Oops, a couple more. Soon this post will be #1 on Geneious link. Damn, another one, I can't resist ...
You're so smart that in your head I'm smarter than I actually am in my own.
I'm not that smarter than you, please.
Geneious is a great software, but not for sequence alignment.
On a somewhat different topic than the above discussion, I used Staden for contig editing and sequence assembly as another alternative to Sequencher [backed with a custom MySQL db for specimens and sequences and custom script to organize all this]. It has the advantage of being completely free and open source, but it isn't as user-friendly or feature-rich as Geneious. Were I starting today, I'm not sure which I'd use, though lately I've been going towards maximizing time in the time/money tradeoff (though closed source science software is unfortunate, especially when many of its features comes from wrapping free open source software).
Thanks for the tip Brian. I'd love to do this stuff with free software, but I don't think there's a free alternative out there that comes close to matching Geneious' functionality and ease of use. As far as the time/money trade-off, I think I'm winning on both fronts. Because much of this work is being done by my technician, I would have had to train him to use the other platforms prior to starting this project. I'm quite certain this would have cost more than the $500 I spent on Geneious Pro. I don't think I'd be able to have undergraduates sequencing at all if I didn't have a relatively easy to use platform for them to work with...
I agree that Geneious is a great program. And what's wrong anyway with a person plugging their favourite software on their own blog anyway??
Yeah, I was also a bit puzzled by the 'not-for-sequence-alignment' baiting by the Anony Mouse. Geneious enables multiple sequence alignment with MUSCLE, which is known to perform very well under simulation (see, e.g., here). Typically, the accuracy of MUSCLE is comparable to that of Mafft and ProbCons, while running much (3-50 times) faster.
Although I don't use Geneious, and am not a fan of the commercial software model, at least the developers of this product are actual scientists working in our field.
Yep - you can tell it's had serious input during development from the sort of people who actually have to use this kind of software.
They're also very responsive to feedback for new features/use-ability. I often see their stall at conferences and you can rock up and chat. Complete opposite of the program I was using (Vector NTI by Invitrogen - did good stuff, but quite complicated, and so hard to get help when things went wrong).
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