Files

• Build.PL
• Changes
• LICENSE
• MANIFEST
• META.json
• META.yml
• README.md
• cpanfile
• doc/Karyotype.md
• doc/Scer-self.md
• doc/Scer.md
• doc/fig.multi.png
• doc/fig.multi.vsd
• lib/App/Egaz.pm
• lib/App/Egaz/Command/blastlink.pm
• lib/App/Egaz/Command/blastmatch.pm
• lib/App/Egaz/Command/blastn.pm
• lib/App/Egaz/Command/exactmatch.pm
• lib/App/Egaz/Command/fas2vcf.pm
• lib/App/Egaz/Command/formats.pm
• lib/App/Egaz/Command/lastz.pm
• lib/App/Egaz/Command/lav2axt.pm
• lib/App/Egaz/Command/lav2psl.pm
• lib/App/Egaz/Command/lpcnam.pm
• lib/App/Egaz/Command/masked.pm
• lib/App/Egaz/Command/maskfasta.pm
• lib/App/Egaz/Command/multiz.pm
• lib/App/Egaz/Command/normalize.pm
• lib/App/Egaz/Command/partition.pm
• lib/App/Egaz/Command/plottree.pm
• lib/App/Egaz/Command/prepseq.pm
• lib/App/Egaz/Command/raxml.pm
• lib/App/Egaz/Command/repeatmasker.pm
• lib/App/Egaz/Command/template.pm
• lib/App/Egaz/Common.pm
• minil.toml
• script/egaz
• share/check_dep.sh
• share/circos.conf.tt2
• share/header.tt2
• share/karyotype/Atha.karyo.tsv
• share/karyotype/karyotype.3702.txt
• share/matrix/default
• share/matrix/distant
• share/matrix/similar
• share/matrix/similar2
• share/parameters.yml
• share/plot_tree.R
• t/01-basic.t
• t/02-commands.t
• t/03-exactmatch.t
• t/04-lav2axt.t
• t/05-lav2psl.t
• t/06-formats.t
• t/07-maskfasta.t
• t/08-masked.t
• t/09-partition.t
• t/10-normalize.t
• t/11-raxml.t
• t/12-plottree.t
• t/13-blastn.t
• t/14-lastz.t
• t/15-prepseq.t
• t/16-lpcnam.t
• t/17-multiz.t
• t/18-repeatmasker.t
• t/19-blastmatch.t
• t/20-blastlink.t
• t/21-fas2vcf.t
• t/91-template.t
• t/Q_rubra.multi.fas
• t/Q_rubravsQ_aliena/mafSynNet/NC_020152.synNet.maf.gz
• t/Q_rubravsQ_aquifolioides/mafSynNet/NC_020152.synNet.maf.gz
• t/Q_rubravsQ_baronii/mafSynNet/NC_020152.synNet.maf.gz
• t/Quercus.nwk
• t/S288c.chr.sizes
• t/YDL184C.fas
• t/YDL184C.nwk
• t/default.lav
• t/default.psl
• t/default.relative.lav
• t/example.fas
• t/lav.tar.gz
• t/partition.q.lav
• t/partition.q.norm.lav
• t/partition.t.lav
• t/partition.t.norm.lav
• t/pig2.blast
• t/pig2.fa
• t/pig2.fa[10001,18000]
• t/pseudocat.fa
• t/pseudocat.fa[5001,10100]
• t/pseudocat/cat.fa
• t/pseudocat/cat.fa[1,10100]
• t/pseudocat/cat.fa[10001,18803]
• t/pseudocat/chr.2bit
• t/pseudocat/chr.sizes
• t/pseudopig.fa
• t/pseudopig/chr.2bit
• t/pseudopig/chr.sizes
• t/pseudopig/pig1.fa
• t/pseudopig/pig1.fa[1,10000]
• t/pseudopig/pig1.fa[10001,20000]
• t/pseudopig/pig1.fa[20001,22929]
• t/pseudopig/pig2.fa
• t/pseudopig/pig2.fa[1,10000]
• t/pseudopig/pig2.fa[10001,20000]
• t/pseudopig/pig2.fa[20001,22929]