Script1.R
Script 1 is the first 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 1 from the manuscript is as follows: Demultiplexed DNA sequences were merged using BBmerge (Bushnell et al. 2017) then processed with TSSV (Anvar et al. 2014) called from FDStools 1.2.0 (Hoogenboom et al. 2017) and then well-represented sequences were selected from the TSSV output using a custom R (R Core Team 2021) script (script 1, datastore). The custom R script selected sequences that had at least 30 % the number of reads of the highest read number recovered for each sample and primer pair, and were at least 50 bp in length, at least 60 % of the maximum read length, retaining no sequences if the highest number of identical reads was < 50. Sequences retained by script 1 were aligned using Muscle (Edgar 2004) and any gaps coded using 2matrix (Salinas and Little 2014).
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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 | 11 |
| Total downloads | 11 |
| Format | unknown |
| License | License Not Specified |
| Version | |
| Datastore active | False |
| Has views | False |
| Id | 58e5242b-d9f1-4474-abad-735dba2aec92 |
| Package id | 9f7064b5-69ff-4431-8673-1c7d22e34708 |
| Position | 2 |
| Size | 2.5 KiB |
| State | active |
| Url type | upload |