NAME

App::Egaz - Backend of Easy Genome Aligner

SYNOPSIS

egaz <command> [-?h] [long options...]
        -? -h --help  show help

Available commands:

    commands: list the application's commands
        help: display a command's help screen

      blastn: blastn wrapper between two fasta files
  exactmatch: exact matched positions in genome sequences
     formats: formats of files use in this project
       lastz: lastz wrapper for two genomes or self alignments
     lav2axt: convert .lav files to .axt files
     lav2psl: convert .lav files to .psl files
      lpcnam: the pipeline of pairwise lav-psl-chain-net-axt-maf
      masked: masked (or gaps) regions in fasta files
   maskfasta: soft/hard-masking sequences in a fasta file
   normalize: normalize lav files
   partition: partitions fasta files by size
    plottree: use the ape package to draw newick trees
     prepseq: preparing steps for lastz
       raxml: raxml wrapper to construct phylogenetic trees

Run egaz help command-name for usage information.

DESCRIPTION

App::Egaz is the backend of Easy Genome Aligner.

Caution: egaz lpcnam implement UCSC's chain-net pipeline, but some parts, e.g. axtChain don't work correctly under macOS. Use egaz lastz's build in chaining mechanism (C=2) instead.

INSTALLATION

cpanm --installdeps https://github.com/wang-q/App-Egaz/archive/0.0.11.tar.gz
curl -fsSL https://raw.githubusercontent.com/wang-q/App-Egaz/master/share/check_dep.sh | bash
cpanm -nq https://github.com/wang-q/App-Egaz/archive/0.0.11.tar.gz
# cpanm -nq https://github.com/wang-q/App-Egaz.git

EXAMPLE

Procedures of multiple genome alignments

Detailed/alternative steps for Saccharomyces cerevisiae strains https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md

AUTHOR

Qiang Wang <wang-q@outlook.com>

LICENSE

This software is copyright (c) 2018 by Qiang Wang.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.