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Operating blocked fasta files
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README.md

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NAME

App::Fasops - operating blocked fasta files

SYNOPSIS

fasops <command> [-?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
     concat: concatenate sequence pieces in blocked fasta files
  consensus: create consensus from blocked fasta file
     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
   mergecsv: merge csv files based on @fields
      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 per-alignment files
       stat: basic statistics on alignments
     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.

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