slphyx / abiapp Goto Github PK

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")

install.packages("devtools")
devtools::install_github("slphyx/ABIApp")

install.packages("devtools")
library(devtools)
install_github("slphyx/ABIApp")

ABI::run_app_ABI()

library(ABI)
run_app_ABI()

ABI_Helminth()
ABI_Helminth(0.06)
ABI_Helminth(0.02,"NS","18S rRNA")
ABI_Helminth(distance = 0.5,group = "CE",marker = "ITS2")

library(ape)
sequences <- read.dna("file.fasta",format = "fasta")
# Convert sequences to distance matrix
dist_matrix <- dist.dna(sequences, model = "raw")

# Construct neighbor-joining tree
nj_tree <- nj(dist_matrix)
genetic_distance <- cophenetic(nj_tree)

# set column and row name
colM <- colnames(genetic_distance)
rowM <- rownames(genetic_distance)

# select taxa
distance_selected  <- genetic_distance[rowM[1],colM[2]]
# Use ABI_Helminth()
ABI_Helminth(distance = distance_selected,
group = "CE",marker = "ITS2")