Caviomorpha phylogenetic tree of extinct and extant taxa

🐹 Building a tree of some small fluffy animals!

Construction supermatrix of biological sequences for phylogenetic analysis for "Caviomorpha", families: Hystricidae, Chinchillidae, Dinomyidae, Abrocomidae, Octodontidae, Ctenomyidae and Echimyidae.

Process

1. Download GenBank (0_restez.R)
2. Identify clusters (1_phylotar.R)
3. Choose clusters (2_cluster.R)
4. Align sequences (3_alignment.R)
5. Construct supermatrix (4_supermatrix.R)
6. Construct ML phylogeny (5_phylogeny.R)
7. Parse results for export (6_parse.R)

All stage scripts can be found in stages/.

Key packages

• restez
• phylotaR
• outsider
• gaius

(All packages are part of the supersmartR project.)

Key programs

• pasta
• MAFFT
• PartitionFinder
• RAxML
• NCBI BLAST+

Methods

Detailed method description can be found in this Google Document.

Results

Download

Download results.zip

(Read the README.md file containted in the zipped folder to learn about the file content.)

Preview

Target taxon