.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5. .TH KALIGNFMT "1" "November 2022" "kalignfmt 3.3.4" "User Commands" .SH NAME kalignfmt \- Global and progressive multiple sequence alignment .SH SYNOPSIS .B kalignfmt-avx2 \fI\,-i -o \/\fR .SH DESCRIPTION Kalign (3.3.4) .SH OPTIONS .TP \fB\-\-format\fR : Output format. [Fasta] .TP \fB\-\-reformat\fR : Reformat existing alignment. [NA] .TP \fB\-\-changename\fR : Change sequence names to 1 .. N. [NA] .TP \fB\-\-unalign\fR : Remove gaps and write to fasta. [NA] .TP \fB\-\-clean\fR : Perform additional checks on alignment. [NA] .TP \fB\-\-version\fR (\fB\-V\fR/\-v) : Prints version. [NA] .SH EXAMPLES Passing sequences via stdin: .IP cat input.fa | kalign \-f fasta > out.afa .PP Combining multiple input files: .IP kalign seqsA.fa seqsB.fa seqsC.fa \-f fasta > combined.afa .SH COPYRIGHT Copyright \(co 2006,2019,2020,2021 Timo Lassmann .PP This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign \fB\-showw\fR'. .br This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. .SS "Please cite:" .IP Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795