Script2.R
Script 2 is the second of 3 custom R scripts used in the paper Prebble JM, Smissen RD, Davis C and Podolyan A. Clarifying subspecies boundaries in Pimelea villosa Sol. ex Sm. (Thymeleaceae) using novel genetic markers: implications for taxonomy and conservation. The scripts were written by Rob Smissen. The description of Script 2 from the manuscript is as follows: Phylip files output by 2matrix were converted to fasta format using the perl script Phylip2Fasta.pl (Hughes unpublished, available at https://github.com/josephhughes/Sequence-manipulation) and further formatted using a custom R script (script2, datastore) and phylogenetic trees for each marker built using the Neighbour-Joining algorithm in MEGA v. 7 (Kumar et al. 2016) to identify highly divergent sequences which were interpreted as non-homologous. Highly divergent sequences were removed using TREE2FASTA 1.4 (Sauvage et al. 2018).
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Additional Information
| Field | Value |
|---|---|
| Data last updated | 22 June 2026 |
| Metadata last updated | 22 June 2026 |
| Created | 22 June 2026 |
| Recent downloads | 9 |
| Total downloads | 13 |
| Format | R |
| License | License Not Specified |
| Version | |
| Datastore active | False |
| Has views | False |
| Id | be3b9a64-e6f2-4d53-852a-ebfcb1385194 |
| Package id | 9f7064b5-69ff-4431-8673-1c7d22e34708 |
| Position | 3 |
| Size | 2 KiB |
| State | active |
| Url type | upload |