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StrainPhlAn
Home > Analysis Platform > StrainPhlAn
Introduction：

StrainPhlAn is a computational tool for tracking individual strains across a large set of samples. The input of StrainPhlAn is a set of metagenomic samples and for each species, the output is a multiple sequence alignment (MSA) file of all species strains reconstructed directly from the samples. From this MSA, StrainPhlAn calls (PhyloPhlAn)[http://segatalab.cibio.unitn.it/tools/phylophlan3/index.html] to build the phylogenetic tree showing the strain evolution of the sample strains.

Workflow Case Analysis Versions Manual Download

https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4

  1. Marker Extraction: Identifies species of interest via MetaPhlAn 4 profile; extracts aligned marker reads from BAM files.

  2. Consensus Building: Generates per-sample consensus sequences for each marker gene.

  3. Alignment & Filtering: Aligns consensus markers across samples; removes low-coverage/recombinant regions.

  4. Phylogeny Inference: Constructs maximum-likelihood tree using RAxML/IQ-TREE.

  5. Output: Produces phylogenetic tree, SNP matrix, and strain abundance table.

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