# How to draw a beautiful evolutionary tree

**URL:** <https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010>\
**Category:** PhyloPhlAn\
**Created:** [September 12, 2020, 1:56pm UTC](https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010 "2020-09-12T13:56:10Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![CK\_zhu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ck_zhu/32/151_2.png) [@CK\_zhu](https://forum.biobakery.org/u/CK_zhu)\
**Post date:** [September 12, 2020, 1:56pm UTC](https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010/1 "2020-09-12T13:56:10Z")

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Dear Francesco

When I run example2 ,I get data result file `input_genomes.tre.treefile`  
Then I want to visual this tree, How can I find the phylum annotation about GCA\_\* files?

```auto
less input_genomes
GCA_001823915.fna.gz  
GCA_002773335.fna.gz
GCA_000520875.fna.gz  
GCA_001567325.fna.gz  
...
GCA_001823925.fna.gz  
GCA_002773355.fna.gz
GCA_000521385.fna.gz  

```

`zcat GCA_*.fna.gz|grep ">"` give me the some info about species,

```auto
>CP019368.1 Borrelia turicatae 91E135 plasmid lpT39, complete sequence
>CP019369.1 Borrelia turicatae 91E135 plasmid lpU43, complete sequence
>CP000061.1 Aster yellows witches'-broom phytoplasma AYWB strain AY-WB chromosome, complete genome
>CP000062.1 Aster yellows witches'-broom phytoplasma AYWB strain AY-WB plasmid pAYWB-I, complete sequence
>CP000063.1 Aster yellows witches'-broom phytoplasma AYWB strain AY-WB plasmid pAYWB-II, complete sequence
>CP000064.1 Aster yellows witches'-broom phytoplasma AYWB strain AY-WB plasmid pAYWB-III, complete sequence
>CP000065.1 Aster yellows witches'-broom phytoplasma AYWB strain AY-WB plasmid pAYWB-IV, complete sequence
>CP000082.1 Psychrobacter arcticus 273-4, complete genome
>CP000096.1 Chlorobium luteolum DSM 273, complete genome
>CP000100.1 Synechococcus elongatus PCC 7942, complete genome
>CP000101.1 Synechococcus elongatus PCC 7942 plasmid 1, complete sequence
>CP000102.1 Methanosphaera stadtmanae DSM 3091, complete genome
>CP000109.2 Thiomicrospira crunogena XCL-2, complete genome
>CP000115.1 Nitrobacter winogradskyi Nb-255, complete genome

```

How can I map species to phylum like following?

```auto
GCA_001823915.fna.gz d __Bacteria.p__ Acidobacteria.c __Acidobacteria.o__ Acidobacte...
GCA_002773335.fna.gz d __Bacteria.p__ Acidobacteria.c __Acidobacteria.o__ Acidobacte...

```

Can you tell me how the following picture is drawn？  
Looking forward to your answer

Chengkai

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/440378da7f0b7118bb9d2d85212ac19c6b7f412c.png)

---

<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [September 14, 2020, 8:59am UTC](https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010/2 "2020-09-14T08:59:27Z")

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Dear Chengkai,

If you followed [PhyloPhlAn 3.0: Example 02: Tree of life](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3.0:-Example-02:-Tree-of-life), you should have run the following command:

```
phylophlan_get_reference -g all \
    -o input_genomes/ \
    -n 1 \
    --verbose 2>&1 | tee logs/phylophlan_get_reference.log

```

The above command should have downloaded a file named `taxa2genomes_cpa201901_up201901.txt.bz2` which contains exactly the taxonomic information you’re looking for.

---

<div class="post-metadata">

**Author:** ![mars](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mars/32/1295_2.png) [@mars](https://forum.biobakery.org/u/mars)\
**Post date:** [April 2, 2022, 7:21am UTC](https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010/3 "2022-04-02T07:21:22Z")

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But how to generate this beautiful tree? Any specific tree editor that shows a beautiful tree like the above?

---

<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [April 8, 2022, 11:50am UTC](https://forum.biobakery.org/t/how-to-draw-a-beautiful-evolutionary-tree/1010/4 "2022-04-08T11:50:24Z")

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In the aboce case, we used GraPhlAn, but you can use any tree visualization tool of your choice. Please, have a look here: [PhyloPhlAn 3.0: Example 02: Tree of life · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3.0:-Example-02:-Tree-of-life#step-3-reconstruct-the-prokaryotes-tree-of-life), where you can find a list of available tools.

Many thanks,  
Francesco