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Commit 62e9392b authored by Fanny Wegner's avatar Fanny Wegner
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Update file phylo_exercise.md

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* The singularity image for `snippy` is here
```
/shares/amr.imm.uzh/bioinfo/singularity/snippy_4.6.0--hdfd78af_2.sif
/shares/amr.imm.uzh/bioinfo/singularity/sandbox/snippy_4.6.0--hdfd78af_2
```
* **How to run snippy:**
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* We will work with the clean.full.aln. First, we want the alignment without the reference. You can do that in many ways. One option is to use `seqtk`, a handy toolbox for sequence analysis. The singularity image can be found here:
```
/shares/amr.imm.uzh/bioinfo/singularity/seqtk_1.3--h7132678_4.sif
/shares/amr.imm.uzh/bioinfo/singularity/sandbox/seqtk-1.3
```
The command we want to use is called `subseq` which extracts all fasta sequences that are specified in an input text file (`samples.ls`):
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The singularity image for `IQtree` can be found here:
```
/shares/amr.imm.uzh/bioinfo/singularity/iqtree_2.2.0.3--hb97b32f_1.sif
/shares/amr.imm.uzh/bioinfo/singularity/sandbox/iqtree_2.2.0.3
```
The basic command structure is the following:
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