HIV sequence database

TreeRate

Purpose: To find a root of a phylogenetic tree and estimate the evolutionary rate(s), by either outgrouping, or single or multiple time point optimization.

How to use: Paste or upload a tree file in standard Newick format and choose a rooting method. To calculate the evolutionary rate, time point data must also be provided. For details, see TreeRate Explanation.

Input

Paste your Newick tree [Sample Input]
Or upload Newick tree file
Or put job number

Rooting method

References

Please reference these articles when using TreeRate:

Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases. 2007 J Virol 81:10625-10635.
Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno W, Korber B, Kuiken C, Ribeiro R, Leitner T. A simple method for optimizing the root in phylogenetic trees with longitudinal data reveals an evolutionary rate that tracks the epidemiological dynamics of HIV-1. 2009 Epidemics 1(4): 230-239.

last modified: Mon Mar 21 16:12 2016

Questions or comments? Contact us at seq-info@lanl.gov.

Index of all tools	Genome Browser	PrimerDesign-M
Alignment Slicer	Heatmap	Protein Feature Accent
AnalyzeAlign	Hepitope	Quality Control
AnnotateTree	Highlighter	QuickAlign
Branchlength	HIV BLAST	Rainbow Tree
CATNAP	HIVAlign	Recombinant HIV-1 Drawing Tool
Codon Alignment	Hypermut	RIP
CombiNAber	jpHMM at GOBICS	SeqPublish
Consensus Maker	Mosaic Vaccine Tool Suite	Sequence Locator
ELF	Motif Scan	SNAP
ElimDupes	N-Glycosite	SUDI Subtyping
Entropy	PCOORD	SynchAlign
Epigraph	PepMap	Translate
FindModel	PeptGen	TreeMaker
Format Converter	PhyloPlace	TreeRate
Gap Strip/Squeeze	PhyML	Variable Region Characteristics
GenBank Entry Generation	Pixel	VESPA
Gene Cutter	Poisson-Fitter	External Tools