Recently in Reed's Life Category

Quiet Times

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This have been quite here because I have been focusing my energy on work and family. To simplify things, I’m going to focus nearly all of my blogging on the Panda’s Thumb for the time being.

The Working Life

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I apologize for things being slow on this blog. I’ve been knee deep in programming, manuscripts, grant proposals, and teaching. I’m hoping to have results to share in the near future. In the mean time, you can follow some of my activities on the Panda’s Thumb.

I will say that the development version of Dawg now supports codon models, and Ngila has some new features as well.

Network Issues

We’ve been having network issues for the last week. (The network setup in general is not reliable.) Nothing is wrong with what I have control over, but I’m kind of stuck with the connection that I’ve been given.

My apologies to everyone this affects.


It’s snowing right now in Houston. I’m not sure if it will stick.

Happy Happy Joy Joy

I need to head home early today to clean up my otaku pad.

I have a girl coming over for a sleep over.

I Have a Minon


We’ve hired a master’s student to be my minion in the lab. Bwahaha…


We’re having network issues which explains why this machine has been off the net since yesterday. It’s working now. Hopefully it will stay that way.

Alive in Houston

Well I’ve moved to Houston and my server is back online.


I’m moving to Houston this weekend. Expect this website and other I administer to have limited functionality for about a week.

When things just work.


I’m moving to Houston next month, and I’m working furiously to finish up about 4 papers before I leave. Yesterday was a good day because two things worked absolutely perfectly.

I’m calculating the likelihoods of some of our observations and I wrote a specific routine to do it for a first-order model. I then wrote a generic routine to calculated likelihoods for higher-order models. When I used the generic routine to calculate the likelihood for a first-order model, I got the same result as my specialized routine. Yatah!

From previous analysis using partial autocorrelations, we determined that a third-order model should explain our data the best. When I compared our models to see which one was most parsimonious (using AIC), the third-order model again came out on top. Yatah2!


I haven’t blogged here in a while, but I do have some recent posts on Panda’s Thumb.

I’ve been busy recently. I’ve flown to Oxford and Montreal for postdoc interviews. I’m also preparing a poster for SMBE in Iowa and a talk for Evolution in Idaho.

I’m currently on vacation. We went snorkeling in Florida: Wakulla Springs, Ginnie Springs, Santa Fe River, Ichetucknee River, and Rainbow Springs.

Across the Pond

I’m flying across the Atlantic for my first time today. I have an interview on Monday in England. I’ll be back in Raleigh on Tuesday, so I won’t have much time to sight-see. But I should have some pictures. Unfortunately, Prof. Steve Steve is not traveling with me this time.

We Hath Frozen Over


It’s Obama’s first day in office, and he has already cured global warming.




My latest paper has now been published by MBE. You can grab your free reprint by following this link. I earlier blogged about some of the implications of this research, which you can see here.


Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a data set of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic data sets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12-16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6-1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.

Reference: Cartwright RA (2009) Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution. 26(7):473–480

Birthday Cake

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For my birthday last month, Tiffany made me a tasty cake, and I’ve finally “developed” the pictures.


I’ve already spent some of my birthday money on LittleBigPlanet.

The Big Three-O

To celebrate the day of my birth, MBE issued the advanced access version of my manuscript: “Problems and solutions for estimating indel rates and length distributions” (pdf) and the supplement.

In Pressed


I found out today that my manuscript, “Problems and Solutions for Estimating Indel Rates and Length Distributions” was accepted for publication in Molecular Biology and Evolution. Yay! I can update that line in my CV.

Speaking of CVs, I’ve applied to over thirty open faculty positions this year. I have no idea how competitive I am for any of them.

I’m not doing a computer poll this week because nothing really happened last week. With the Texas Tech-Oklahoma show down this week, the top of the rankings is going to get very interesting.

And we got snow flurries today.

And Fallout 3 rocks.

Free Day


Took the day off work.

Voted Early.

Tried to explain to a senior citizen that she shouldn’t be afraid of voter fraud.

Went to the state fair.

Watched draft horse competition.

Drank smoothie.

Watched Hereford bull competition.

Looked at champion goats and sheep.

Ate steak sandwich with Coke.

Looked at championship rabbits.

Drank lemonade.

Watched more draft horses competition.

Watched trick bike show.

Ate roasted turkey leg.

Rode Ferris wheel.

Rode the Zipper with screaming wife.

Ate deep fried Snickers with Coke.

Saw championship arts and crafts.

Went home.

Wrote blog post.


I just returned from putting Tiffany on an Amtrak overnight to Orlando. On Friday, I’ll catch a plane to Minnesota for the Evolution conference, where we’ll be able to have a mini howler fest.

Pwned by Evolution


Tiffany was pwned by evolution this morning when she got three wisdom teeth removed.


She is currently resting while I tend to her every thirty minutes for the next six hours.

I’m sure many of you know what she is going through. I had all four of my wisdom teeth removed in high school, but I hardly remember a thing because of the horse pills that I was taking for the pain.

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