# Tutorial: Phylogenetic Codon Tree Service

## Overview
This set of short videos provides a step-by-step demonstration of using the PATRIC Phylogenetic Codon Tree Service to construct a codon-based phylogenetic tree from a set of genomes.

1. [Creating genome groups for building codon trees (16:54)](#codon1)
2. [Submitting the tree-building job (11:38)](#codon2)
3. [Reviewing the codon tree report (11:31)](#codon3)
4. [Accessing codon tree files in the jobs folder (10:58)](#codon4)
5. [Removing problem genomes from groups (15:42)](#codon5)
6. [Using the Protein Family Sorter to improve the tree (15:35)](#codon6)
7. [Viewing the tree in FigTree (7:17)](#codon7)
8. [Finding help and citing (8:50)](#codon8)

### See also
* [Phylogenetic Tree Service](https://patricbrc.org/app/PhylogeneticTree)
* [Phylogenetic Codon Tree Service Tutorial](https://docs.patricbrc.org/tutorial/codon_tree_building/codon_tree_building.html) (document)

## Using the Phylogenetic Codon Tree Building Service

Links to the videos are provided below.  They can also be viewed in order in the [PATRIC YouTube channel playlist](https://www.youtube.com/playlist?list=PLsstVALeacEIj7YA33V4nYi10oOZgEVDq). Relevant references are provided at the bottom of this page.

<a name="codon1"></a>
##### 1. Creating genome groups for building codon trees (16:54)
<iframe width="560" height="315" src="https://www.youtube.com/embed/TzTyQcSz7bQ" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon2"></a>
##### 2. Submitting the tree-building job (11:38)
<iframe width="560" height="315" src="https://www.youtube.com/embed/EVIwNDoK6HI" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon3"></a>
##### 3. Reviewing the codon tree report (11:31)
<iframe width="560" height="315" src="https://www.youtube.com/embed/3ED2aX412dg" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon4"></a>
##### 4. Accessing codon tree files in the jobs folder (10:58)
<iframe width="560" height="315" src="https://www.youtube.com/embed/BuwPNJXcIJI" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon5"></a>
##### 5. Removing problem genomes from groups (15:42)
<iframe width="560" height="315" src="https://www.youtube.com/embed/qPBQV1UNPzU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon6"></a>
##### 6. Using the Protein Family Sorter to improve the tree (15:35)
<iframe width="560" height="315" src="https://www.youtube.com/embed/tg27Z3Btk8I" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon7"></a>
##### 7. Viewing the tree in FigTree (7:17)
<iframe width="560" height="315" src="https://www.youtube.com/embed/K6dNUVHsHAw" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

<a name="codon8"></a>
##### 8. Finding help and citing (8:50)
<iframe width="560" height="315" src="https://www.youtube.com/embed/DDWPcJLgWr0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## References
* Cock, P.J., et al., Biopython: freely available Python tools for computational molecular biology and bioinformatics. 2009. 25(11): p. 1422-1423.
* Davis, J.J., et al., PATtyFams: Protein families for the microbial genomes in the PATRIC database. 2016. 7: p. 118.
* Edgar, R.C.J.N.a.r., MUSCLE: multiple sequence alignment with high accuracy and high throughput. 2004. 32(5): p. 1792-1797.
* Letunic, I. and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic acids research, 2016. 44(W1): p. W242-W245.
* Rambaut, A.J.S.h.t.b.e.a.u.s.f., FigTree, a graphical viewer of phylogenetic trees. 2007.
* Stamatakis, A.J.B., RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. 2014. 30(9): p. 1312-1313.
* Stamatakis, A., P. Hoover, and J.J.S.b. Rougemont, A rapid bootstrap algorithm for the RAxML web servers. 2008. 57(5): p. 758-771.