staden-2.0.0b11-i586-1_slonly.txz


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Description

staden - DNA sequence assembly, editing, and analysis tools

Distribution: Slackware 14.2
Repository: Slackonly i486
Package name: staden
Package version: 2.0.0b11
Package release: 1_slonly
Package architecture: i586
Package type: txz
Installed size: 11.04 MB
Download size: 3.36 MB
Official Mirror: packages.slackonly.com
The programs of the Staden package offer excellent and fully developed set of DNA sequence assembly, editing, analysis tools and more. Home: http://staden.sourceforge.net/ References: /usr/doc/staden-2.0.0b11/References

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Requires

    Download

    Source package: unknown

    Install Howto

    1. Download staden-2.0.0b11-i586-1_slonly.txz
    2. Install staden txz package:
      # upgradepkg --install-new staden-2.0.0b11-i586-1_slonly.txz

    Files

    • /install/doinst.sh
    • /install/slack-desc
    • /install/slack-required
    • /usr/
    • /usr/bin/alfsplit
    • /usr/bin/copy_db
    • /usr/bin/copy_reads
    • /usr/bin/create_emboss_files
    • /usr/bin/eba
    • /usr/bin/find_renz
    • /usr/bin/gap4
    • /usr/bin/gap5
    • /usr/bin/gap5_cmd
    • /usr/bin/getABISampleName
    • /usr/bin/getABIcomment
    • /usr/bin/getABIdate
    • /usr/bin/getABIfield
    • /usr/bin/get_scf_field
    • /usr/bin/hetins
    • /usr/bin/init_exp
    • /usr/bin/make_weights
    • /usr/bin/mutscan
    • /usr/bin/polyA_clip
    • /usr/bin/prefinish
    • /usr/bin/pregap4
    • /usr/bin/qclip
    • /usr/bin/screen_seq
    • /usr/bin/spin
    • /usr/bin/staden_convert
    • /usr/bin/stash
    • /usr/bin/stops
    • /usr/bin/tg_index
    • /usr/bin/tg_index.bin
    • /usr/bin/tracediff
    • /usr/bin/trev
    • /usr/bin/vector_clip
    • /usr/doc/
    • /usr/doc/staden-2.0.0b11/ChangeLog
    • /usr/doc/staden-2.0.0b11/LICENCE.txt
    • /usr/doc/staden-2.0.0b11/NEWS
    • /usr/doc/staden-2.0.0b11/README.build
    • /usr/doc/staden-2.0.0b11/References
    • /usr/doc/staden-2.0.0b11/staden.SlackBuild
    • /usr/lib/
    • /usr/lib/staden/libcopy_reads.so
    • /usr/lib/staden/libg.so
    • /usr/lib/staden/libgap.so
    • /usr/lib/staden/libgap5.so
    • /usr/lib/staden/libhaplo.so
    • /usr/lib/staden/libmisc.so
    • /usr/lib/staden/libmutlib.so
    • /usr/lib/staden/libprefinish.so
    • /usr/lib/staden/libprimer3.so
    • /usr/lib/staden/libseq_utils.so
    • /usr/lib/staden/libspin.so
    • /usr/lib/staden/libtext_utils.so
    • /usr/lib/staden/libtk_utils.so
    • /usr/share/
    • /usr/share/applications/gap4.desktop
    • /usr/share/applications/gap5.desktop
    • /usr/share/applications/pregap4.desktop
    • /usr/share/applications/spin.desktop
    • /usr/share/applications/trev.desktop
    • /usr/share/pixmaps/gap4.png
    • /usr/share/pixmaps/gap5.png
    • /usr/share/pixmaps/pregap4.png
    • /usr/share/pixmaps/spin.png
    • /usr/share/pixmaps/trev.png
    • /usr/share/staden/staden.profile
    • /usr/share/staden/etc/2bars_h.bmp
    • /usr/share/staden/etc/2bars_v.bmp
    • /usr/share/staden/etc/GTAGDB
    • /usr/share/staden/etc/NOTEDB
    • /usr/share/staden/etc/RENZYM.4
    • /usr/share/staden/etc/RENZYM.6
    • /usr/share/staden/etc/RENZYM.ALL
    • /usr/share/staden/etc/align_lib_nuc_matrix
    • /usr/share/staden/etc/cap2rc
    • /usr/share/staden/etc/cap3rc
    • /usr/share/staden/etc/checked.gif
    • /usr/share/staden/etc/config.prefinish
    • /usr/share/staden/etc/copy_readsrc
    • /usr/share/staden/etc/eia.wts
    • /usr/share/staden/etc/emboss_menu
    • /usr/share/staden/etc/fak2rc
    • /usr/share/staden/etc/follow.bitmap
    • /usr/share/staden/etc/gap5rc
    • /usr/share/staden/etc/gap5rc_menu_full
    • /usr/share/staden/etc/gaprc
    • /usr/share/staden/etc/gaprc_menu_full
    • /usr/share/staden/etc/gaprc_menu_mito
    • /usr/share/staden/etc/haplorc
    • /usr/share/staden/etc/help_config
    • /usr/share/staden/etc/ied.wts
    • /usr/share/staden/etc/m13mp18_primers
    • /usr/share/staden/etc/niprc
    • /usr/share/staden/etc/nuc_matrix
    • /usr/share/staden/etc/pam250
    • /usr/share/staden/etc/perceptron.wts
    • /usr/share/staden/etc/phraprc
    • /usr/share/staden/etc/prefinishrc
    • /usr/share/staden/etc/pregap4rc
    • /usr/share/staden/etc/prokprom_10.wts
    • /usr/share/staden/etc/prokprom_35.wts
    • /usr/share/staden/etc/renzyme_bairoch
    • /usr/share/staden/etc/shlib.conf
    • /usr/share/staden/etc/siprc
    • /usr/share/staden/etc/spin_embossrc
    • /usr/share/staden/etc/spinrc
    • /usr/share/staden/etc/tk_utilsrc
    • /usr/share/staden/etc/trevrc
    • /usr/share/staden/etc/unchecked.gif
    • /usr/share/staden/etc/vector_primer
    • /usr/share/staden/etc/alus/ALUA
    • /usr/share/staden/etc/alus/HUMA1ATP
    • /usr/share/staden/etc/alus/HUMACHRA7
    • /usr/share/staden/etc/alus/HUMADAG
    • /usr/share/staden/etc/alus/HUMADAG-10
    • /usr/share/staden/etc/alus/HUMADAG-11
    • /usr/share/staden/etc/alus/HUMADAG-12
    • /usr/share/staden/etc/alus/HUMADAG-13
    • /usr/share/staden/etc/alus/HUMADAG-14
    • /usr/share/staden/etc/alus/HUMADAG-15
    • /usr/share/staden/etc/alus/HUMADAG-16
    • /usr/share/staden/etc/alus/HUMADAG-17
    • /usr/share/staden/etc/alus/HUMADAG-18
    • /usr/share/staden/etc/alus/HUMADAG-2
    • /usr/share/staden/etc/alus/HUMADAG-3
    • /usr/share/staden/etc/alus/HUMADAG-4
    • /usr/share/staden/etc/alus/HUMADAG-5
    • /usr/share/staden/etc/alus/HUMADAG-6
    • /usr/share/staden/etc/alus/HUMADAG-7
    • /usr/share/staden/etc/alus/HUMADAG-8
    • /usr/share/staden/etc/alus/HUMADAG-9
    • /usr/share/staden/etc/alus/HUMAGG
    • /usr/share/staden/etc/alus/HUMALBG
    • /usr/share/staden/etc/alus/HUMALBG-2
    • /usr/share/staden/etc/alus/HUMANFA
    • /usr/share/staden/etc/alus/HUMANFA-2
    • /usr/share/staden/etc/alus/HUMAPOAI1
    • /usr/share/staden/etc/alus/HUMAPOAI1-2
    • /usr/share/staden/etc/alus/HUMAPOAII
    • /usr/share/staden/etc/alus/HUMAPOAII-2
    • /usr/share/staden/etc/alus/HUMAPOCII
    • /usr/share/staden/etc/alus/HUMAPOE4
    • /usr/share/staden/etc/alus/HUMAPOE4-2
    • /usr/share/staden/etc/alus/HUMAPOE4-3
    • /usr/share/staden/etc/alus/HUMAPOE4-4
    • /usr/share/staden/etc/alus/HUMBLYM1
    • /usr/share/staden/etc/alus/HUMC1A21
    • /usr/share/staden/etc/alus/HUMC1A23
    • /usr/share/staden/etc/alus/HUMC1AIN1
    • /usr/share/staden/etc/alus/HUMERPA
    • /usr/share/staden/etc/alus/HUMFIXG
    • /usr/share/staden/etc/alus/HUMFIXG-2
    • /usr/share/staden/etc/alus/HUMFIXG-3
    • /usr/share/staden/etc/alus/HUMFIXG-4
    • /usr/share/staden/etc/alus/HUMFOL5
    • /usr/share/staden/etc/alus/HUMFOL5-2
    • /usr/share/staden/etc/alus/HUMGAST2
    • /usr/share/staden/etc/alus/HUMGHV
    • /usr/share/staden/etc/alus/HUMHBA4
    • /usr/share/staden/etc/alus/HUMHBA4-2
    • /usr/share/staden/etc/alus/HUMHBA4-3
    • /usr/share/staden/etc/alus/HUMHBBRT
    • /usr/share/staden/etc/alus/HUMHBBRT-2
    • /usr/share/staden/etc/alus/HUMIFNB3
    • /usr/share/staden/etc/alus/HUMIFNB3-2
    • /usr/share/staden/etc/alus/HUMIFNB3-3
    • /usr/share/staden/etc/alus/HUMIFNB3-4
    • /usr/share/staden/etc/alus/HUMIFNB3-5
    • /usr/share/staden/etc/alus/HUMIL2R8
    • /usr/share/staden/etc/alus/HUMINS2
    • /usr/share/staden/etc/alus/HUMLDLIVS
    • /usr/share/staden/etc/alus/HUMLDLR
    • /usr/share/staden/etc/alus/HUMLDLR-2
    • /usr/share/staden/etc/alus/HUMMHDC3B
    • /usr/share/staden/etc/alus/HUMMHDRB3
    • /usr/share/staden/etc/alus/HUMMHDRB3-2
    • /usr/share/staden/etc/alus/HUMMYCRT
    • /usr/share/staden/etc/alus/HUMNGFB
    • /usr/share/staden/etc/alus/HUMPOMC
    • /usr/share/staden/etc/alus/HUMPOMC-2
    • /usr/share/staden/etc/alus/HUMPOMC1
    • /usr/share/staden/etc/alus/HUMPOMC2
    • /usr/share/staden/etc/alus/HUMPOMC6
    • /usr/share/staden/etc/alus/HUMRSA1
    • /usr/share/staden/etc/alus/HUMRSA16
    • /usr/share/staden/etc/alus/HUMRSA27
    • /usr/share/staden/etc/alus/HUMRSAB11
    • /usr/share/staden/etc/alus/HUMRSAB13
    • /usr/share/staden/etc/alus/HUMRSAB19
    • /usr/share/staden/etc/alus/HUMRSAB2
    • /usr/share/staden/etc/alus/HUMRSAB6
    • /usr/share/staden/etc/alus/HUMRSAB8
    • /usr/share/staden/etc/alus/HUMRSAOLD
    • /usr/share/staden/etc/alus/HUMRSAP3
    • /usr/share/staden/etc/alus/HUMRSKA1
    • /usr/share/staden/etc/alus/HUMRSKPA1
    • /usr/share/staden/etc/alus/HUMSLJT1
    • /usr/share/staden/etc/alus/HUMTBB5
    • /usr/share/staden/etc/alus/HUMTBB5-2
    • /usr/share/staden/etc/alus/HUMTBB5-3
    • /usr/share/staden/etc/alus/HUMTBB5-4
    • /usr/share/staden/etc/alus/HUMTBB5-5
    • /usr/share/staden/etc/alus/HUMTBB5-6
    • /usr/share/staden/etc/alus/HUMTBB5-7
    • /usr/share/staden/etc/alus/HUMTBBM40
    • /usr/share/staden/etc/alus/HUMTHBNB
    • /usr/share/staden/etc/alus/HUMTHBNB-2
    • /usr/share/staden/etc/alus/HUMTHBNB-3
    • /usr/share/staden/etc/alus/HUMTPA
    • /usr/share/staden/etc/alus/HUMTPA-10
    • /usr/share/staden/etc/alus/HUMTPA-11
    • /usr/share/staden/etc/alus/HUMTPA-12
    • /usr/share/staden/etc/alus/HUMTPA-13
    • /usr/share/staden/etc/alus/HUMTPA-14
    • /usr/share/staden/etc/alus/HUMTPA-15
    • /usr/share/staden/etc/alus/HUMTPA-16
    • /usr/share/staden/etc/alus/HUMTPA-17
    • /usr/share/staden/etc/alus/HUMTPA-18
    • /usr/share/staden/etc/alus/HUMTPA-19
    • /usr/share/staden/etc/alus/HUMTPA-2
    • /usr/share/staden/etc/alus/HUMTPA-20
    • /usr/share/staden/etc/alus/HUMTPA-21
    • /usr/share/staden/etc/alus/HUMTPA-22
    • /usr/share/staden/etc/alus/HUMTPA-3
    • /usr/share/staden/etc/alus/HUMTPA-4
    • /usr/share/staden/etc/alus/HUMTPA-5
    • /usr/share/staden/etc/alus/HUMTPA-6
    • /usr/share/staden/etc/alus/HUMTPA-7
    • /usr/share/staden/etc/alus/HUMTPA-8
    • /usr/share/staden/etc/alus/HUMTPA-9
    • /usr/share/staden/etc/alus/HUMUG2PD
    • /usr/share/staden/etc/alus/HUMUG2PD-2
    • /usr/share/staden/etc/alus/M11591
    • /usr/share/staden/etc/alus/M12036
    • /usr/share/staden/etc/alus/M12929
    • /usr/share/staden/etc/alus/M13121
    • /usr/share/staden/etc/alus/README
    • /usr/share/staden/etc/alus/consensi
    • /usr/share/staden/etc/alus/fasta-split
    • /usr/share/staden/etc/alus/files
    • /usr/share/staden/etc/alus/filesp
    • /usr/share/staden/etc/blast_data/BLOSUM62
    • /usr/share/staden/etc/blast_data/ecoli.nhr
    • /usr/share/staden/etc/blast_data/ecoli.nin
    • /usr/share/staden/etc/blast_data/ecoli.nsq
    • /usr/share/staden/etc/blast_data/gc.val
    • /usr/share/staden/etc/blast_data/seqcode.val
    • /usr/share/staden/etc/gcodes/code_1
    • /usr/share/staden/etc/gcodes/code_10
    • /usr/share/staden/etc/gcodes/code_11
    • /usr/share/staden/etc/gcodes/code_12
    • /usr/share/staden/etc/gcodes/code_13
    • /usr/share/staden/etc/gcodes/code_14
    • /usr/share/staden/etc/gcodes/code_15
    • /usr/share/staden/etc/gcodes/code_16
    • /usr/share/staden/etc/gcodes/code_2
    • /usr/share/staden/etc/gcodes/code_21
    • /usr/share/staden/etc/gcodes/code_22
    • /usr/share/staden/etc/gcodes/code_23
    • /usr/share/staden/etc/gcodes/code_3
    • /usr/share/staden/etc/gcodes/code_4
    • /usr/share/staden/etc/gcodes/code_5
    • /usr/share/staden/etc/gcodes/code_6
    • /usr/share/staden/etc/gcodes/code_9
    • /usr/share/staden/etc/gcodes/code_index
    • /usr/share/staden/etc/vectors/lorist6.seq
    • /usr/share/staden/etc/vectors/m13mp18.seq
    • /usr/share/staden/etc/vectors/pBS.seq
    • /usr/share/staden/etc/vectors/pOTW13.seq
    • /usr/share/staden/etc/vectors/pgem3zfm.seq
    • /usr/share/staden/etc/vectors/pgem3zfp.seq
    • /usr/share/staden/etc/vectors/pgem5zfm.seq
    • /usr/share/staden/etc/vectors/psc194.seq
    • /usr/share/staden/etc/vectors/puc18.seq
    • /usr/share/staden/scripts/assemble4
    • /usr/share/staden/scripts/fasta-split
    • /usr/share/staden/scripts/fasta2exp
    • /usr/share/staden/scripts/finish_cDNA
    • /usr/share/staden/scripts/finish_cDNA_ends_only
    • /usr/share/staden/scripts/finish_sanger
    • /usr/share/staden/scripts/splitseq_da
    • /usr/share/staden/scripts/staden_help
    • /usr/share/staden/tcl/
    • /usr/share/staden/tcl/copy_reads/copy_reads.tcl
    • /usr/share/staden/tcl/copy_reads/copy_reads_main.tcl
    • /usr/share/staden/tcl/copy_reads/tclIndex
    • /usr/share/staden/tcl/gap/acd2tag.tcl
    • /usr/share/staden/tcl/gap/alter_rel.tcl
    • /usr/share/staden/tcl/gap/assemble_direct.tcl
    • /usr/share/staden/tcl/gap/auto_assemble.tcl
    • /usr/share/staden/tcl/gap/break_contig.tcl
    • /usr/share/staden/tcl/gap/check_assembly.tcl
    • /usr/share/staden/tcl/gap/clip.tcl
    • /usr/share/staden/tcl/gap/complement.tcl
    • /usr/share/staden/tcl/gap/confidence_graph.tcl
    • /usr/share/staden/tcl/gap/configure.tcl
    • /usr/share/staden/tcl/gap/consen.tcl
    • /usr/share/staden/tcl/gap/consistency_display.tcl
    • /usr/share/staden/tcl/gap/contig_editor.tcl
    • /usr/share/staden/tcl/gap/contig_id.tcl
    • /usr/share/staden/tcl/gap/contig_order.tcl
    • /usr/share/staden/tcl/gap/contig_selector.tcl
    • /usr/share/staden/tcl/gap/dis_readings.tcl
    • /usr/share/staden/tcl/gap/dstrand.tcl
    • /usr/share/staden/tcl/gap/editor_search.tcl
    • /usr/share/staden/tcl/gap/enter_tags.tcl
    • /usr/share/staden/tcl/gap/extract.tcl
    • /usr/share/staden/tcl/gap/fij.tcl
    • /usr/share/staden/tcl/gap/find_oligo.tcl
    • /usr/share/staden/tcl/gap/find_repeats.tcl
    • /usr/share/staden/tcl/gap/gap.tcl
    • /usr/share/staden/tcl/gap/gap_canvas_box.tcl
    • /usr/share/staden/tcl/gap/gap_nav.tcl
    • /usr/share/staden/tcl/gap/gap_prefinish.tcl
    • /usr/share/staden/tcl/gap/gap_restriction_enzymes.tcl
    • /usr/share/staden/tcl/gap/gap_utils.tcl
    • /usr/share/staden/tcl/gap/help_exp.tcl
    • /usr/share/staden/tcl/gap/list_contigs.tcl
    • /usr/share/staden/tcl/gap/list_proc.tcl
    • /usr/share/staden/tcl/gap/ng_fb_cmds.tcl
    • /usr/share/staden/tcl/gap/notes.tcl
    • /usr/share/staden/tcl/gap/oligo_param.tcl
    • /usr/share/staden/tcl/gap/pcr_primers.tcl
    • /usr/share/staden/tcl/gap/preass.tcl
    • /usr/share/staden/tcl/gap/probe.tcl
    • /usr/share/staden/tcl/gap/qual.tcl
    • /usr/share/staden/tcl/gap/quality_plot.tcl
    • /usr/share/staden/tcl/gap/reactions.tcl
    • /usr/share/staden/tcl/gap/reading_coverage.tcl
    • /usr/share/staden/tcl/gap/readpair.tcl
    • /usr/share/staden/tcl/gap/readpair_coverage.tcl
    • /usr/share/staden/tcl/gap/result_manager.tcl
    • /usr/share/staden/tcl/gap/search.tcl
    • /usr/share/staden/tcl/gap/select_contig.tcl
    • /usr/share/staden/tcl/gap/sendto.tcl
    • /usr/share/staden/tcl/gap/show_relationships.tcl
    • /usr/share/staden/tcl/gap/shuffle_pads.tcl
    • /usr/share/staden/tcl/gap/stop_codon.tcl
    • /usr/share/staden/tcl/gap/strand_coverage.tcl
    • /usr/share/staden/tcl/gap/tag_checklist.tcl
    • /usr/share/staden/tcl/gap/tag_editor.tcl
    • /usr/share/staden/tcl/gap/tclIndex
    • /usr/share/staden/tcl/gap/template_display.tcl
    • /usr/share/staden/tcl/gap/trace_display.tcl
    • /usr/share/staden/tcl/gap5/acd2tag.tcl
    • /usr/share/staden/tcl/gap5/assemble_single.tcl
    • /usr/share/staden/tcl/gap5/break_contig.tcl
    • /usr/share/staden/tcl/gap5/check_assembly.tcl
    • /usr/share/staden/tcl/gap5/check_database.tcl
    • /usr/share/staden/tcl/gap5/complement.tcl
    • /usr/share/staden/tcl/gap5/configure.tcl
    • /usr/share/staden/tcl/gap5/consen.tcl
    • /usr/share/staden/tcl/gap5/contig_editor.tcl
    • /usr/share/staden/tcl/gap5/contig_extend.tcl
    • /usr/share/staden/tcl/gap5/contig_graph.tcl
    • /usr/share/staden/tcl/gap5/contig_id.tcl
    • /usr/share/staden/tcl/gap5/contig_selector.tcl
    • /usr/share/staden/tcl/gap5/depth.tcl
    • /usr/share/staden/tcl/gap5/dis_readings.tcl
    • /usr/share/staden/tcl/gap5/editor_search.tcl
    • /usr/share/staden/tcl/gap5/export_contigs.tcl
    • /usr/share/staden/tcl/gap5/fij.tcl
    • /usr/share/staden/tcl/gap5/find_oligo.tcl
    • /usr/share/staden/tcl/gap5/find_repeats.tcl
    • /usr/share/staden/tcl/gap5/gap4_compat.tcl
    • /usr/share/staden/tcl/gap5/gap5.tcl
    • /usr/share/staden/tcl/gap5/gap5_cmd.tcl
    • /usr/share/staden/tcl/gap5/gap5_del_test.tcl
    • /usr/share/staden/tcl/gap5/gap5_thrash.tcl
    • /usr/share/staden/tcl/gap5/gap_canvas_box.tcl
    • /usr/share/staden/tcl/gap5/gap_globals.tcl
    • /usr/share/staden/tcl/gap5/gap_restriction_enzymes.tcl
    • /usr/share/staden/tcl/gap5/gap_utils.tcl
    • /usr/share/staden/tcl/gap5/import_contigs.tcl
    • /usr/share/staden/tcl/gap5/import_gff.tcl
    • /usr/share/staden/tcl/gap5/jog.tcl
    • /usr/share/staden/tcl/gap5/libraries.tcl
    • /usr/share/staden/tcl/gap5/list_contigs.tcl
    • /usr/share/staden/tcl/gap5/list_proc.tcl
    • /usr/share/staden/tcl/gap5/map_reads.tcl
    • /usr/share/staden/tcl/gap5/ng_fb_cmds.tcl
    • /usr/share/staden/tcl/gap5/qual.tcl
    • /usr/share/staden/tcl/gap5/readpair.tcl
    • /usr/share/staden/tcl/gap5/replay_log.tcl
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