Travis Wheeler

32 Campus Dr
Social Sciences Bldg. Room 412
Missoula MT 59812
Curriculum Vitae


My group develops methods in computational biology, with an emphasis on sequence analysis - (1) development of algorithms that increase the speed and power of homology search using profile hidden Markov models, (2) implementation of those methods in the highly-used HMMER homology search toolkit, and (3) application of these methods to biology-motivated topics, especially those involving transposable elements and regulatory elements.

The lab has open positions for motivated postdocs and PhD students. Please drop me a line if you'd like to discuss possibilities.

See what we've been talking about in our lab meetings recently.


Department of Computer Science (Assistant Professor)
Cellular, Molecular, and Microbial Biology (Associated Faculty)
LBNL / Joint Genome Institute (Affiliate)


For full-page view, click here
Schedule time with me

Recent News (from my blog)


Bill Arndt (Joint with Kjiersten Fagnan at JGI/NERSC)
HMMER vectorization
PhD students
Walt Shands (Computer Science)
Translated search in HMMER
Masters students
Alex Nord (Computer Science)
Sequence search in HMMER (esp. seed-based acceleration, spaced seeds)
Undergraduate students
Eric Wall (Biology / Computer Science)
Conserved non-coding elements

Gilia Patterson (Biology)
Transposable element annotation

Michel Wan Der Maas Soares (Computer Science)
Fast phylogeny inference

Emily Cheroske (Computer Science)
Homology search - seed-based acceleration of protein search
High school students
Joyce Liu
Sequence alignment guide trees


CSCI 323 (Design and Analysis of Algorithms)
Spring 2016
CSCI 480 / CSCI 580 (Applied Parallel Computing)
Spring 2016
CSCI 451 / CSCI 558 (Computational Biology / Bioinformatics)
Fall 2015
Contact me if you wish to see material from past classes.


The Dfam Database of Repetitive DNA Families (2015) [link]
Hubley, R., Finn, R.D., Clements, J., Eddy, S.R., Jones, T.A., Bao, W., Smit, A.F.A, and Wheeler, T.J. Nucleic Acids Research 46:gkv1272.
A call for benchmarking transposable element annotation methods. (2015) [link]
Hoen, D.R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A-S., Hua-Van, A., Hubley, R., Kapusta, A., Lerat, E., Maumus, F., Pollock, D.D., Quesneville, H., Smit, A., Wheeler, T.J., Bureau, T.E., Blanchette, M. Mobile DNA, 6(1):1-9.
HMMER web server: 2015 update. (2015) [link]
Finn, R.D., Clements, J., Arndt, W., Miller, B.L., Wheeler, T.J., Schreiber, F., Bateman, A., and Eddy, S.R. Nucleic Acids Research 43(W1):W30-W38.
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. (2014) [link]
Wheeler, T.J., Clements, J., and Finn, R.D. BMC Bioinformatics, 15:7.
Distinguished as a “Highly Accessed Article”.
nhmmer: DNA homology search with profile HMMs. (2013) [link]
Wheeler, T.J., Eddy, S.R. Bioinformatics, 29(19):2487–2489.
(doi: 10.1093/bioinformatics/btt403)
In the top 20 most-read Bioinformatics articles during September 2013.
Dfam: a database of repetitive DNA based on profile hidden Markov models. (2013) [link]
Wheeler, T.J., Clements, J., Eddy, S.R., Hubley, R., Jones, T.A., Jurka, J., Smit, A.F.A, and Finn, R.D. Nucleic Acids Research 41:D70–D82.
(doi: 10.1093/nar/gks1265)
Selected as an NAR Featured Article.
Estimating the accuracy of multiple alignments and its use in parameter advising. (2012) [link]
DeBlasio, D., Wheeler, T., and Kececioglu, J. Proceedings of the 16th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics, 7262: 45-59.
(doi: 10.1007/978-3-642-29627-7_5)
Complete nucleomorph genome sequence of the non-photosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. (2010) [link]
Tanifuji, G. Onodera, N.T., Wheeler, T.J., Dlutek, M., Donaher, N., and Archibald, J.M. Genome Biology and Evolution, 3: 44-54.
(doi: 10.1093/gbe/evq082)
Aligning protein sequences with predicted secondary structure. (2010) [link]
Kececioglu, J., Kim, E., and Wheeler, T. Journal of Computational Biology, 17(3): 561-580.
Selected as a "recommended read" for Faculty of 1000 Biology.
Efficient construction of accurate multiple alignments and large-scale phylogenies. (2009) [link]
Wheeler, T.J.
Ph.D. dissertation
Department of Computer Science, University of Arizona, Tucson, Arizona.
Large-scale neighbor-joining with NINJA. (2009) [link, preprint]
Wheeler, T.J. Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI), 375-389.
(doi: 10.1007/978-3-642-04241-6_31)
Learning models for aligning protein sequence with predicted secondary structure. (2009) [link]
Kim, E., Wheeler, T.J., and Kececioglu, J.D. Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics, 5541: 586-605.
(doi: 10.1007/978-3-642-02008-7_36)
Multiple alignment by aligning alignments. (2007) [link]
Wheeler, T.J. and Kececioglu, J.D. Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics, 23: i559-i568.
(doi: 10.1093/bioinformatics/btm226)
Adaptive protein evolution and regulatory divergence in Drosophila. (2006) [link]
Good, J.M., Hayden, C.A., and Wheeler T.J. Molecular Biology and Evolution, 23(6): 1101-1103.
(doi: 10.1093/molbev/msk002)
Evaluating and improving cDNA sequence quality with cQC. (2005) [link]
Hayden, C.A., Wheeler, T.J., and Jorgensen R.A. Bioinformatics, 21(24): 4414-4415.
(doi: 10.1093/bioinformatics/bti709)
Transposable element orientation bias in the Drosophila melanogaster genome. (2005) [link]
Cutter, A.D, Good, J.M., Pappas, C.T., Saunders, M.A., Starrett, D.M., Wheeler T.J. Journal of Molecular Evolution, 61(6): 733-741.
(doi: 10.1007/s00239-004-0243-0)

Software and databases

Skylign Logo server [link]
A tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler, T.J., Clements, J., Finn, R.D.
HMMER webserver, and HMMER3.1 [link]
Biological sequence analysis using profile hidden Markov models.
Eddy, S.R. and Wheeler, T.J.
nhmmer [link] (within HMMER3.1)
A DNA-DNA sequence homology search tool based on profile hidden Markov models, in the HMMER3 framework.
Wheeler, T.J. and Eddy, S.R.
Dfam [link]
A Database of Repetitive DNA Based on Profile Hidden Markov Models.
Wheeler, T.J., Clements, J., Eddy, S.R., Hubley, R., Jones, T.A., Jurka, J., Smit, A.F.A, Finn, R.D.
Ninja [link].
A Mesquite package for fast neighbor-joining phylogeny inference.
Wheeler, T.J. and Maddison, D.R.
NINJA [link]
Software for large-scale neighbor-joining phylogeny inference.
Wheeler ,T.J.
Opalescent [link]
A Mesquite package for multiple sequence alignment.
Wheeler, T.J. and Maddison, D.R.
Opal [link]
Software for multiple sequence alignment by optimally aligning alignments.
Wheeler ,T.J. and Kececioglu. J.D.
Align [link]
A Mesquite package for aligning sequence data.
Maddison, D.R., Wheeler, T.J., and Maddison, W.P.
AlignAlign [link]
Software for optimally aligning alignments.
Starrett, D.M., Wheeler, T.J., and Kececioglu, J.D.
cQC - cDNA Quality Control [link]
A tool for resolving putative sequencing errors in single-pass cDNA, based on genomic sequence.
Hayden, C.A. and Wheeler, T.J.