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HFV Ebola sequence database
 

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PhyML Explanation

Input

This web interface takes as input an alignment in any standard format.

Substitution Models

On this interface, the default evolutionary model for nucleotide data is GTR + gamma (designed for sequences with significant between-site rate heterogeneity, such as HIV). The default evolutionary model for protein data is HIVb (designed for between-patient HIV-1 data). These models may not be suitable for your data! We recommend first testing your data with FindModel for DNA, or with ProtTest for protein. For additional information about evolutionary models, see references below.

Mailback

This web interface will send your results by e-mail if any of the following are true:

File sizes for bootstrapping

Bootstrapping puts a high load on web servers. We recommend the following maximums:

# BootstrapsMax. filesize
02M
100100K
50050K
100010K

From the PhyML manual:

(For the full PhyML manual, see PhyML 3.0 User Guide.)

References for Substitution Models:

Nucleotide
Model
Reference
HKY85 Hasegawa M, Kishino H, Yano T (1985). "Dating of human-ape splitting by a molecular clock of mitochondrial DNA". Journal of Molecular Evolution 22: 160–174.
JC69Jukes TH and Cantor CR (1969). Evolution of Protein Molecules. New York: Academic Press. pp. 21–132.
K80Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120
F81Felsenstein J (1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach". Journal of Molecular Evolution 17: 368–376
F84(Felsenstein, 1989)
TN93 Tamura K, Nei M (1993). "Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees". Molecular Biology and Evolution 10 (3): 512–526.
GTRTavaré S (1986). "Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences". Lectures on Mathematics in the Life Sciences (American Mathematical Society) 17: 57–86.

Amino acid
Model
Reference
Blosum62"Amino acid substitution matrices from protein blocks." Henikoff S. & Henikoff J. PNAS 89, 10915–10919 (1992).
CpREV"Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA." Adachi J.P.W., Martin W. & Hasegawa M. Journal of Molecular Evolution 50, 348–358 (2000).
Dayhoff"A model of evolutionary change in proteins." Dayhoff M., Schwartz R. & Orcutt B. In Dayhoff, M. (ed.) Atlas of Protein Sequence and Structure, vol. 5, 345–352 (National Biomedical Research Foundation, Washington, D. C., 1978).
DCMut"Different versions of the Dayhoff rate matrix." Kosiol C. & Goldman N. Molecular Biology and Evolution 22, 193–19 (2004).
FLU
HIVb
HIVw
Nickle, D.C., Heath, L., Jensen, M.A., Gilbert, P.B., Mullins, J.I., and Kosakovsky Pond, S.L. 2007. HIV-specific probabilistic models of protein evolution. PLoS ONE 2: e503
JTT"The rapid generation of mutation data matrices from protein sequences." Jones D., Taylor W. & Thornton J. Computer Applications in the Biosciences (CABIOS) 8, 275–282 (1992).
LG"An improved general amino-acid replacement matrix." Le S. & Gascuel O. Mol. Biol. Evol. 25(7):1307-20 (2008
MtArtAbascal, F., Posada, D., and Zardoya, R. 2007. MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol 24: 1-5
MtMam"Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders." Cao Y. et al. Journal of Molecular Evolution 47, 307–322 (1998)
MtREV
RtREV"rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny." Dimmic M., Rest J., Mindell D. & Goldstein D. Journal of Molecular Evolution 55, 65–73 (2002).
VT"Modeling amino acid replacement." Muller T. & Vingron M. Journal of Computational Biology 7, 761–776 (2000).
WAG"A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach." Whelan S. & Goldman N. Mol. Biol. Evol. 18, 691–699 (2001)



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