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HIV Sequence Database



Neighbor TreeMaker

Purpose: This tool takes a nucleotide sequence alignment, converts it to NEXUS format, and uses PAUP to generate a tree, which is displayed using the R Project ape package.

Details: After sequence input, the next page will give additional options. Gaps can be treated as missing or stripped. The user can choose from various distance models and select the outgroup sequence. A version of the input alignment in which the sequences have been reordered to match the order in the tree may be downloaded. Trees are calculated using the neighbor-joining method. You can use FindModel to decide what evolutionary model best fits your data.

Disclaimer: This interface offers a basic, rapid phylogenetic analysis using neighbor joining as implemented in PAUP. Sequences are clustered in a tree according to sequence distances. Maximum likelihood trees are likely to give more accurate phylogenetic reconstructions, but are much more computationally expensive. For more information see the Tree Tutorial.

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

Tree parameters
Include reference sequences (HIV-1/CPZ only)

Maximum likelihood tree generating tools

last modified: Tue Sep 19 14:28 2017


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

 
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