[![Build Status](https://travis-ci.org/wang-q/App-Fasops.svg?branch=master)](https://travis-ci.org/wang-q/App-Fasops) [![Coverage Status](http://codecov.io/github/wang-q/App-Fasops/coverage.svg?branch=master)](https://codecov.io/github/wang-q/App-Fasops?branch=master) [![MetaCPAN Release](https://badge.fury.io/pl/App-Fasops.svg)](https://metacpan.org/release/App-Fasops) # NAME App::Fasops - operating blocked fasta files # SYNOPSIS fasops [-?h] [long options...] -? -h --help show help Available commands: commands: list the application's commands help: display a command's help screen axt2fas: convert axt to blocked fasta check: check genome locations in (blocked) fasta headers covers: scan blocked fasta files and output covers on chromosomes join: join multiple blocked fasta files by common target links: scan blocked fasta files and output bi/multi-lateral range links maf2fas: convert maf to blocked fasta names: scan blocked fasta files and output all species names refine: realign blocked fasta file with external programs replace: replace headers from a blocked fasta separate: separate blocked fasta files by species slice: extract alignment slices from a blocked fasta split: split blocked fasta files to separate per-alignment files subset: extract a subset of species from a blocked fasta xlsx: paint substitutions and indels to an excel file See `fasops commands` for usage information. # AUTHOR Qiang Wang <wang-q@outlook.com> # COPYRIGHT AND LICENSE This software is copyright (c) 2014 by Qiang Wang. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.