View source: R/AllPairwiseAlign.R
AllPairwiseAlign | R Documentation |
This function is a wrapper function to compute all pairwise (global) alignments using VSEARCH.
AllPairwiseAlign( file, cores = 1, mask = "none", out.name = "AllPairwiseAlign", output = NULL )
file |
path to fasta file storing sequences for which all possible pairwise alignments shall be computed. |
cores |
number of cores that shall be used for parallel computations. |
mask |
shall the aligned sequences be maksed? Options are: |
out.name |
name of the output files ( |
output |
path to a folder in which output shall be stored. |
To be able to use this function the VSEARCH command line tool needs to be installed.
A folder named vsearch_pairwise_align
will be created and the following files will be stored in this output folder:
*.uc
USEARCH cluster format generated by VSEARCH storing the sequence cluster information of aligned sequences.
*_userout.txt
a tab separated file storing the alignment information in the columns: query
, target
, sequence identity (ID)
.
*.blast6out
BLAST output format of the pairwise (global) sequence alignments generated by VSEARCH.
*_fasta_pairs.fasta
fasta file storing the alignments.
*.sam
SAM file storing the alignments.
Hajk-Georg Drost
https://github.com/torognes/vsearch
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