drwxr-xr-x root/root usr/ drwxr-xr-x root/root usr/lib/ drwxr-xr-x root/root usr/lib/R/ drwxr-xr-x root/root usr/lib/R/library/ drwxr-xr-x root/root usr/lib/R/library/gggenomes/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/DESCRIPTION -rw-r--r-- root/root usr/lib/R/library/gggenomes/INDEX -rw-r--r-- root/root usr/lib/R/library/gggenomes/LICENSE drwxr-xr-x root/root usr/lib/R/library/gggenomes/Meta/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/Rd.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/data.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/features.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/hsearch.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/links.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/nsInfo.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/Meta/package.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/NAMESPACE drwxr-xr-x root/root usr/lib/R/library/gggenomes/R/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/R/gggenomes -rw-r--r-- root/root usr/lib/R/library/gggenomes/R/gggenomes.rdb -rw-r--r-- root/root usr/lib/R/library/gggenomes/R/gggenomes.rdx drwxr-xr-x root/root usr/lib/R/library/gggenomes/data/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/data/Rdata.rdb -rw-r--r-- root/root usr/lib/R/library/gggenomes/data/Rdata.rds -rw-r--r-- root/root usr/lib/R/library/gggenomes/data/Rdata.rdx drwxr-xr-x root/root usr/lib/R/library/gggenomes/exec/ -rwxr-xr-x root/root usr/lib/R/library/gggenomes/exec/gb2gff -rwxr-xr-x root/root usr/lib/R/library/gggenomes/exec/seq-len drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/ drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/MT/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT-human.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT-minimap1-minidot.pdf -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT-minimap1-sensitive.paf -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT-orang.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT.paf -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/MT/MT.png drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/cafeteria/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cafeteria/CrBVI.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cafeteria/CrCflag.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cafeteria/CrE410P.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cafeteria/CrRCC970.fa drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/cyanophages/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/P-SSP3.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/P-SSP3.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/P-SSP7.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/P-SSP7.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP1.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP1.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP2.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP2.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP3.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP3.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP42.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S-CBP42.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S05-C243.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S05-C243.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S08-C41.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/S08-C41.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/SS120-1.fa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/SS120-1.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/cyanophages/cyano.paf -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/eden-utr.gff drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/emales/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-MCP.afa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-MCP.nwk drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/emales-MCP.afa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/emales-cds.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/emales-ngaro.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/emales-tir.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-all/emales.fna -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-cogs.tsv -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-gc.bed -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-ngaros.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-prot-ava.o6 -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-prot-uniref50.tsv -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales-tirs.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.faa -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.fna -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.fna.seqkit.fai -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.gff -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.ids -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/emales/emales.paf drwxr-xr-x root/root usr/lib/R/library/gggenomes/extdata/gorg/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/gorg/gorg-pads-defense.o6 -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/gorg/gorg.fna -rw-r--r-- root/root usr/lib/R/library/gggenomes/extdata/gorg/gorg.gff drwxr-xr-x root/root usr/lib/R/library/gggenomes/help/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/AnIndex -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/aliases.rds drwxr-xr-x root/root usr/lib/R/library/gggenomes/help/figures/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/emales.png -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/logo-slack.pdf -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/logo-slack.png -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/logo-smaller.png -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/logo.png -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/figures/logo.svg -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/gggenomes.rdb -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/gggenomes.rdx -rw-r--r-- root/root usr/lib/R/library/gggenomes/help/paths.rds drwxr-xr-x root/root usr/lib/R/library/gggenomes/html/ -rw-r--r-- root/root usr/lib/R/library/gggenomes/html/00Index.html -rw-r--r-- root/root usr/lib/R/library/gggenomes/html/R.css