hmmSearch: Run hmmsearch (HMMER 3)

In iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny

Description

Takes a fasta file and a Hidden Markov Model profile and performs a search of the former over the latter.

Usage

hmmSearch(fasta, hmm, eval = "1e-10", oty = "domtblout", n_threads = 1L)

Arguments

fasta	A protein fasta file.
hmm	A hmm file. Must be pressed (see hmmpress from HMMER manual).
eval	evalue threshold.
oty	The hmmsearch output type.
n_threads	An integer. The number of cores to use.

Value

The path to a temporary file where the hmmsearch output is placed.

iferres/phylen documentation built on May 24, 2019, 2:04 a.m.