インストール
mac os10.14の miniconda2-4.3.14環境でテストした。
本体 Github
#Anaconda環境でcondaを使い導入
conda install -c bioconda swalign
> swalign
$ swalign
Simple Smith-Waterman aligner
Usage: swalign {options} ref query
Reference and query arguments can either be written on the command-line, read
from stdin, or read as FASTA format files. If there is more than one sequence
in the reference FASTA file, the query will be aligned to all reference
sequences and only the best scoring alignment will be displayed. If more than
one sequence is in a query FASTA file, each query sequence will be aligned to
the reference.
Alignments will be made in both forward and reverse directions.
Options:
-m N Match score (default: 2)
-mm N Mismatch penalty (default: 1)
-gap N Gap penalty (default: 1)
-gapext N Gap extension penalty (default: 1)
-gapdecay N Decay the gap extension penalty (default: 0.0)
-wrap N Wrap alignments when they are longer than N bases
-global Perform a global alignment (experimental)
-query Align the full query sequence (mix of local/global)
-summary fname Write a summary files of match locations (tab-delimited)
-useregion Use regions for coordinates if included in FASTA ref
Example:
~$ swalign AAGGGGAGGACGATGCGGATGTTC AGGGAGGACGATGCGG
実行方法
swalign ref.fa query.fa > align
引用
GitHub - mbreese/swalign: Smith-Waterman local aligner
