App::Egaz - Backend of Easy Genome Aligner
egaz <command> [-?h] [long options...] -? -h --help show help Available commands: commands: list the application's commands help: display a command's help screen blastlink: link sequences by blastn blastmatch: matched positions by blastn in genome sequences blastn: blastn wrapper between two fasta files exactmatch: exact matched positions in genome sequences fas2vcf: list variations in blocked fasta file formats: formats of files use in this project lastz: lastz wrapper for two genomes or self alignments lav2axt: convert .lav files to .axt lav2psl: convert .lav files to .psl 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 multiz: multiz step by step 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 repeatmasker: RepeatMasker wrapper template: create executing bash files
Run egaz help command-name for usage information.
egaz help command-name
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.
egaz lpcnam
axtChain
egaz lastz
C=2
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
egaz template
Qiang Wang <wang-q@outlook.com>
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.
To install App::Egaz, copy and paste the appropriate command in to your terminal.
cpanm
cpanm App::Egaz
CPAN shell
perl -MCPAN -e shell install App::Egaz
For more information on module installation, please visit the detailed CPAN module installation guide.