Tutorial: Phylogenetic Codon Tree Service¶
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.
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. Relevant references are provided at the bottom of this page.
1. Creating genome groups for building codon trees (16:54)¶
2. Submitting the tree-building job (11:38)¶
3. Reviewing the codon tree report (11:31)¶
4. Accessing codon tree files in the jobs folder (10:58)¶
5. Removing problem genomes from groups (15:42)¶
6. Using the Protein Family Sorter to improve the tree (15:35)¶
7. Viewing the tree in FigTree (7:17)¶
8. Finding help and citing (8:50)¶
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.