HIV sequence database

TreeRate beta

Purpose: This tool finds a root of a phylogenetic tree by outgroup, by single time point optimization, or by multiple time point optimization.

How to use: Paste or upload the tree file in standard Newick format, and choose one of the rooting methods. To calculate the evolutionary rate by the minimum sum of variance optimization method, a file of taxa names and time points (years, months or days in decimal form), must also be uploaded (see example). For additional details, see TreeRate Explanation.

Note: This is the beta version of TreeRate, so please send us an e-mail if you have trouble. Thank you for your understanding.

Input

Paste your Newick tree [Sample Input]
	(OR)
Upload Newick tree file

Optional

Upload dates file

Choose rooting method:

Outgroup	Single time point optimization	Multiple time point optimization
Branchlength	LS optimized mid point	Minimum sum of variance optimization
	Standard mid pointing [coming soon!!!!]

E-mail address

(Will be used only if number of taxa > 100)

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.
Athreya G, Maljkovic Berry I, 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. Manuscript submitted.

last modified: Mon Apr 13 14:30 2009

Index of all tools	ADRA	Branchlength
Codon Alignment	Consensus Maker	ELF
ElimDupes	Entropy	Epilign
FindModel	Format converter	Gap strip/squeeze
Gene Cutter	HDent/HDdist	Heatmap
Hepitope	Highlighter	HIV BLAST
HIValign	Hypermutation	jpHMM at GOBICS
Mosaic Vaccine Tool Suite	Motif Scan	N-Glycosite
ODprep/ODfit	PCOORD	PepMap
PeptGen	PhyloPlace	PhyML
Pixel	Primalign	Protein Feature Accent
Protein structure	Quick Align	Recombinant HIV-1 drawing tool
RIP	SeqPublish	Sequence locator
SNAP	SUDI subtyping	SynchAlign
Translate	Treemaker	TreeRate
VESPA	External tools