seqtools/barcodegap.Rmd at main · nikolasjohnston/seqtools · GitHub

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---
title: "species_delimitation"
output: html_notebook
---


```{r}
##install packages if needed
#install.packages("BarcodingR")
#install.packages("adegenet")
#install.packages("ape")

library('BarcodingR')
library('ape')
library('adegenet')

dna_ref <- fasta2DNAbin('barcodes_ref.fasta')

#where reference is formatted like this:
#name in fasta, species name
#e.g.
#>clarki_123_-_COX1_gene, Calliphora_clarki
#>niveata_124_-_COX1_gene, Calliphora_niveata
#>nigristima_125_-_COX1_gene, Calliphora_nigristigma
#>nigristigma_126_-_COX1_gene, Calliphora_nigristigma
#>niveata_130_-_COX1_gene, Calliphora_niveata
#>niveata_131_-_COX1_gene, Calliphora_niveata
#>clarki_132_-_COX1_gene, Calliphora_clarki
#>trojana_133_-_COX1_gene, Calliphora_trojana
#>torjana_134_-_COX1_gene, Calliphora_trojana
#>niveata_138_-_COX1_gene, Calliphora_niveata
#>niveata_243_-_COX1_gene, Calliphora_niveata
#>Xanthocera_286_S3_L00_-_COX1_gene, Calliphora_xanthocera
#>Xanthocera_B3_Consensus_-_COX1_gene, Calliphora_xanthocera
#>Xanthocera_B4_Consensus_-_COX1_gene, Calliphora_xanthocera


dna_query <- fasta2DNAbin('barcodes_file.fasta')
#normal sequence file


b.gap <- barcoding.gap(dna_query, dist = "raw")

b.gap

```