HIV sequence database

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Curated Alignments Special Interest
Alignments

TOOLS

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

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GUIDES

Tutorials CRFs HIV-1 Gene Map In-depth Annotation 3D Structure Data Dictionary How to Cite
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Pixel

Show an image of an alignment with 1 pixel per residue

Purpose: This tool generates an image of an alignment using 1 or more colored pixel(s) for each residue, thus allowing errors in large alignments to be easily seen. See Pixel Explanation.

Input

Paste your alignment here [Sample Input]
or upload your file

Options

Choose sequence type	Guess (by composition) Amino acids DNA
Color scheme	Default Matches gray (relative to first sequence) Matches white, mismatches red, indels black
Scale	(each alignment residue will be a square of this many pixels per side)

Plotting code created by Will Fischer. Interface by Carla Kuiken. See How to cite.

last modified: Wed Apr 25 16:06 2012