# Tut 5: Phylogenetic Trees

A couple of changes to note:

1. You will want to do Mafft on the slurm cluster
2. You'll want to use probably 15-16 Ribosomal proteins instead of just RPS3
3. You'll want to use TrimAI instead of Aliview to do your trimming (more details to come)
4. You'll want to use iqtree instead of fasttree for your tree building. And make sure you do a test of which model is the best fit  to create your tree (see iqtree documentation)

## Powerpoint:

{% file src="/files/4DAhvm7h33z3uplZxPMO" %}

## Tutorial:

Preston has found its easier to drop his doccuments in rather than reformat. Here:

{% file src="/files/nDdV76fr7Oshk06x3Rb1" %}

## Iqtree

{% embed url="<http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2>" %}

eg:&#x20;

{% code overflow="wrap" %}

```
trimal -in /groups/banfield/projects/environmental/EastRiver/Vegtype/Preston/phylogeny/sept23_gtdbtk_out/goosos_out/alignments/curated_drep_vegtype.mfaa -out /groups/banfield/projects/environmental/EastRiver/Vegtype/Preston/phylogeny/sept23_gtdbtk_out/goosos_out/trim_curated_drep_vegtype.mfaa -htmlout curated_drep_vegtype.html -gt 0.05
```

{% endcode %}

use `-gt 0.05` as your criterion, this takes sequences with > 95% gaps in a column (at a single amino acid alignment)


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