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Limit the number of taxa in clades of a taxonomic category: Show taxa per LCA Superkingdom Kingdom Phylum Subphylum Superclass Class Subclass Superorder Order Suborder Superfamily Family Subfamily Genus Subgenus Species Subspecies
You can provide the character delimiter and the field position if the name of each sequence does not correspond to a protein accession.
E.g. for leaf names with the following pattern: gi|4757876|ref|NP_004326.1|, by choosing "|" as delimiter and "1" as field position (0 is the first position), 4757876 will be extracted and considered as a protein accession.
Extract all leaves names on your tree.
You can provide a tab-delimited file containing the leaf name (first column) and the correspondent taxonomy id (second column).
E.g. if you have a Newick tree like this: "(gorilla:2,(chimp:1,4757876:1):1);" you can provide a tab-delimited table with the following content: gorilla 9595chimp 9598You do not need to place the taxonomy ID of 4757876 in the table since it corresponds to a protein accession number.
Midpoint rooting: Find the largest distance between leaves and root at its midpoint.
Taxonomic rooting: Find the branch comprising taxonomically distant leaves. Suited for an experiment in which there is an outgroup sequence taxonomically distant to the rest of sequences.
Enter a jobID and a file type Tree in Nexus Tree in SVG Taxonomy Rep. Alignment Blast result Log file
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TaxOnTree generates a phylogenetic tree in NEXUS format designed to be openned in FigTree. Blast result and sequence alignment are also available for download.
FigTree is available for download here or at FigTree's website.
Here are some NEXUS file generated by TaxOnTree: Sample #1 #2 #3
Instructions for visualizing your tree on FigTree can be found here
Check out the log file to have some clues on what is causing the error.
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Do you have question, suggestion or some trouble using TaxOnTree? Feel free to email us!
TaxOnTree has a command-line version that can be run in a UNIX platform.
If you intend to use TaxOnTree in large scale, please consider downloading the source code in our Sourceforge page. BLAST database used in this webservice are also available there.
Command-line version also allows you to set a custom BLAST database
In this webservice, TaxOnTree takes as input a protein identifier from NCBI or Uniprot databases and has as output a phylogenetic tree in NEXUS format configured to be visualized in FigTree software. Legend: LCA: Lowest Common Ancestor.
Grab the image to zoom it.
TaxOnTree is a bioinformatic tool that automatically colors a phylogenetic tree according to the taxonomical informations obtained from NCBI taxonomy.
By visualizing the phylogenetic tree generated by TaxOnTree you can:
Please check out some screenshots and tree samples in our Gallery.
A scheme of TaxOnTree workflow is showed in How it works?.
Instruction to open and visualize your phylogenetic tree can be found here
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Leaves names will be displayed like this:
Biological data are retrieved from NCBI (Copyright and Disclaimers) and Uniprot