Workflow Type: Galaxy

Estimate 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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Input alignment #main/Input alignment Alignment in fasta format, containing variable positions from variant calling
  • File

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
  • File
Info #main/Info n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:59 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:59

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