Comments on: Paper of the week: INDELible: A Flexible Simulator of Biological Sequence Evolution

By: Paulo Nuin

Paulo Nuin — Tue, 11 Aug 2009 15:01:15 +0000

Nice, Reed. Thanks for your comment, and I’m happy to see Dawg getting the praise it deserves. Keep us posted on new developments on the program and good luck with the new postdoc.

By: Reed A. Cartwright

Reed A. Cartwright — Tue, 11 Aug 2009 04:01:12 +0000

Their target was Dawg. Fletcher and Yang actually tested their program against Dawg to verify that it worked correctly. I was proud to see the number of actual and proposed features of Dawg that they incorporated into their program. They also let me know about a big bug in Dawg, which has been fixed. Yay.

Indelible implments many of the features I’ve been planing for future development of Dawg; however, their code is difficult to follow, and I don’t think any of it can be integrated into Dawg. I’ve discussed collaborating with Yang and Fletcher, and the impression I get is that neither of them are likely to continue developing Indelible.

I’ve started a new postdoc and I’m hoping to be able to devote some time to Dawg. I plan on opening it up to more community development.

By: Paulo Nuin

Paulo Nuin — Mon, 10 Aug 2009 20:56:08 +0000

Ian,

As I mentioned in the post, I’m a little bit removed from simulating sequences. I had yours on my Citulike and noticed that they didn’t compare to your program, which is cited anyway. They also barely compared INDELible to Simprot, an application that I was involved. It seems that their target was DAWG, although they have a nice comparison matrix.

I think the more the merrier for simulation applications. Each one has it strengths and weaknesses, but most of them are under appreciated, what is quite sad.

By: Ian Holmes

Ian Holmes — Mon, 10 Aug 2009 16:23:00 +0000

What about GSimulator/SimGenome?

http://genomebiology.com/2008/9/10/R147