Mtb phylogeny 1.0
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Run on GalaxyEstimate a phylogenetic tree from whole genome sequencing data for M. tuberculosis
Associated Tutorial
This workflows is part of the tutorial Tree thinking for tuberculosis evolution and epidemiology, available in the GTN
Thanks to...
Tutorial Author(s): Christoph Stritt, Daniela Brites, Galo A. Goig
Tutorial Contributor(s): Wolfgang Maier, Helena Rasche, Peter van Heusden, Christoph Stritt, Saskia Hiltemann, Bérénice Batut, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input alignment | #main/Input alignment | Alignment in fasta format, containing variable positions from variant calling |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | RStudio | Use R to visualize a phylogenetic tree interactive_tool_rstudio |
| 2 | Estimate phylogeny with RAxML | Maximum likelihood-based inference of a phylogenetic tree toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Best-scoring ML Tree | #main/Best-scoring ML Tree | n/a |
|
| Info | #main/Info | n/a |
|
Version History
master
Creators and Submitter
Views: 39 Downloads: 5 Runs: 0
Created: 2nd Jun 2025 at 10:59
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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