Phylogenetic Tree Building Service

Overview

The Phylogenetic Tree Building Service enables construction of custom phylogenetic trees for up to 50 user-selected genomes. The service builds trees using conserved protein sequences, which is the same methodology used to build the public genus-level phylogenetic trees in the PATRIC website.The service returns a Newick file which can be downloaded or viewed in html or rendered in the interactive Phylogenetic Tree Viewer in PATRIC.

Using the Phylogenetic Tree Building Service

The Phylogenetic Tree submenu option under the Services main menu (Genomics category) opens the Phylogenetic Tree input form (shown below). Note: You must be logged into PATRIC to use this service.

Phylogenetic Tree Menu

Options

Phylogenetic Tree Input Form

Ingroup Genomes Selection

Select at least 3 genome (up to total of 50 genomes) from the genome list and/or a genome group and use the plus buttons to place the genomes to the table. A genome or genome group CANNOT be placed in both ingroup and outgroup table.

Select Genome

Genomes for inclusion in the ingroup for the tree. Type or select a genome name from the genome list. Use the plus (+) icon to add to the Selected Ingroup Genome Table.

And/Or Select Genome Group

Option for including a genome group from the workspace. Can be included with, or instead of, the Selected Genomes.

Selected Ingroup Genome Table

Genomes chosen for inclusion in the ingroup. Genomes can be removed by clicking the "x" beside the genome name.

Outgroup Genomes

Select at least 1 genome (up to total of 5 genomes) from the genome list and/or a genome group and use the plus buttons to place the genomes to the table. A genome or genome group CANNOT be placed in both ingroup and outgroup table.

Select genome

Genomes for inclusion in the outgroup for the tree. Type or select a genome name from the genome list. Use the plus (+) icon to add to the Selected Outgroup Genome Table.

And/or select genome group

Option for including a genome group from the workspace. Can be included with, or instead of, the Selected Genomes.

Selected Outgroup Genome Table

Genomes chosen for inclusion in the outgroup. Genomes can be removed by clicking the "x" beside the genome name.

Parameters

Output Folder

The workspace folder where results will be placed.

Output Name

Name used to uniquely identify results.

Full Tree Method

This option selects the tree-building method to be used.

FastTree: A less rigorous tree inference program that takes much less time than RAxML while often producing similar trees. FastTree reference

Maximum Likelihood (RAxML): A maximum likelihood tree estimation program. RAxML reference

Automated Progressive Refinement

Option for selecting progressive refinement, which is a method for attempting to improve tree quality by targeted rebuilding of subtrees. Confidently placed subtrees that contain poorly-supported branches are re-analyzed in more detail in an attempt to resolve the less certain branches. Due to the additional rounds of tree building, this option can significantly increase the running time.