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freebsd-ports/biology/consed/pkg-plist.examples
Edwin Groothuis 69ef603a61 New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:00:37 +00:00

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share/examples/consed/assembly_view/edit_dir/.consedrc
share/examples/consed/assembly_view/edit_dir/.consedrc_mini
share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta
share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log
share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1
share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview
share/examples/consed/assembly_view/edit_dir/doNotShowInAssemblyView.fof
share/examples/consed/assembly_view/edit_dir/fragSizes.txt
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1
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share/examples/consed/standard/chromat_dir/djs74-2231.s1
share/examples/consed/standard/chromat_dir/djs74-2350.s1
share/examples/consed/standard/chromat_dir/djs74-2361.s1
share/examples/consed/standard/chromat_dir/djs74-237.s1
share/examples/consed/standard/chromat_dir/djs74-2516.s1
share/examples/consed/standard/chromat_dir/djs74-2664.s1
share/examples/consed/standard/chromat_dir/djs74-2679.s1
share/examples/consed/standard/chromat_dir/djs74-2689.s1
share/examples/consed/standard/chromat_dir/djs74-2931.s1
share/examples/consed/standard/chromat_dir/djs74-3174.s1
share/examples/consed/standard/chromat_dir/djs74-423.s1
share/examples/consed/standard/chromat_dir/djs74-561.s1
share/examples/consed/standard/chromat_dir/djs74-564.s1
share/examples/consed/standard/chromat_dir/djs74-690.x1
share/examples/consed/standard/chromat_dir/djs74-824.s1
share/examples/consed/standard/chromat_dir/djs74-932.s1
share/examples/consed/standard/chromat_dir/djs74-996.s2
share/examples/consed/standard/chromats_to_add/djs74-1455.s1
share/examples/consed/standard/chromats_to_add/djs74-1465.s1
share/examples/consed/standard/chromats_to_add/djs74-2282.s1
share/examples/consed/standard/chromats_to_add/djs74-2712.s1
share/examples/consed/standard/chromats_to_add/djs74-2861.s1
share/examples/consed/standard/chromats_to_add/djs74-536.s2
share/examples/consed/standard/chromats_to_add/djs74-568.s1
share/examples/consed/standard/chromats_to_add/djs74-649.x1
share/examples/consed/standard/chromats_to_add/djs74-867.s1
share/examples/consed/standard/edit_dir/custom_navigation.nav
share/examples/consed/standard/edit_dir/fragSizes.txt
share/examples/consed/standard/edit_dir/reads_to_add.fof
share/examples/consed/standard/edit_dir/reads_to_remove.fof
share/examples/consed/standard/edit_dir/standard.030328.142354.fasta
share/examples/consed/standard/edit_dir/standard.030328.142354.fasta.log
share/examples/consed/standard/edit_dir/standard.contigs
share/examples/consed/standard/edit_dir/standard.contigs.log
share/examples/consed/standard/edit_dir/standard.fasta
share/examples/consed/standard/edit_dir/standard.fasta.log
share/examples/consed/standard/edit_dir/standard.fasta.screen
share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1
share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1.aview
share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs
share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.log
share/examples/consed/standard/edit_dir/standard.fasta.screen.problems
share/examples/consed/standard/edit_dir/standard.fasta.screen.problems.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.singlets
share/examples/consed/standard/edit_dir/standard.fasta.screen.view
share/examples/consed/standard/edit_dir/standard.newtags
share/examples/consed/standard/edit_dir/standard.phrap.out
share/examples/consed/standard/edit_dir/standard.screen.out
share/examples/consed/standard/edit_dir/standardNewChromats.fof
share/examples/consed/standard/edit_dir/standard_to_alu.cross
share/examples/consed/standard/phd_dir/djs74-1180.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1432.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1532.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1802.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1803.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1861.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1871.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2231.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2350.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2361.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-237.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2516.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2664.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2679.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2689.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2931.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-3174.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-423.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-423.s1.phd.2
share/examples/consed/standard/phd_dir/djs74-561.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-564.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-690.x1.phd.1
share/examples/consed/standard/phd_dir/djs74-824.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-932.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-996.s2.phd.1
@dirrm share/examples/consed/assembly_view/chromat_dir
@dirrm share/examples/consed/assembly_view/edit_dir
@dirrm share/examples/consed/assembly_view/phd_dir
@dirrm share/examples/consed/assembly_view
@dirrm share/examples/consed/autofinish/chromat_dir
@dirrm share/examples/consed/autofinish/edit_dir
@dirrm share/examples/consed/autofinish/phd_dir
@dirrm share/examples/consed/autofinish
@dirrm share/examples/consed/polyphred/chromat_dir
@dirrm share/examples/consed/polyphred/edit_dir
@dirrm share/examples/consed/polyphred/phd_dir
@dirrm share/examples/consed/polyphred/poly_dir
@dirrm share/examples/consed/polyphred
@dirrm share/examples/consed/standard/chromat_dir
@dirrm share/examples/consed/standard/chromats_to_add
@dirrm share/examples/consed/standard/edit_dir
@dirrm share/examples/consed/standard/phd_dir
@dirrm share/examples/consed/standard
@dirrm share/examples/consed