## Development script for function guidance
## Last update 2017-03-15
library("ips")
library("foreach")
library("parallel")
library("doSNOW")
library("pbmcapply")
library(polenta)
# 1. Read sequences
ms <- read.fas("dev/data/cortinarius_28s_ms.fas")
set.seed(100)
sequences <- sample(ms, 10) ## choose 10 sequences
ncore = 24
bootstrap = 100
msa.program = "mafft"
method = "auto"
exec = "/usr/local/bin/mafft"
parallel = TRUE
cutoff = 0.93
system.time(test <- guidance(seqs = seqs,
ncore = 24,
bootstrap = 100,
msa.program = "mafft",
method = "auto",
parallel = TRUE,
cutoff = 0.93))
# 15 min with 2 cores
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