academic/archeopteryx: Removed (renamed to archaeopteryx).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

9 files changed, 0 insertions, 619 deletions

diff --git a/academic/archeopteryx/README b/academic/archeopteryx/README
deleted file mode 100644
index ed8730cfab03..000000000000
--- a/academic/archeopteryx/README
+++ /dev/null
@@ -1,11 +0,0 @@
-Archeopteryx: visualise, analyse and edit phylogenetic trees 
- 
-Archeopteryx is a software tool for the visualization, analysis, and
-editing of potentially large and highly annotated phylogenetic trees.
-Archeopteryx (the successor to ATV) is entirely written in the Java
-programming language and is based on the forester libraries.
-
-Please cite:
-Han M.V. and Zmasek C.M. (2009)
-phyloXML: XML for evolutionary biology and comparative genomics
-BMC Bioinformatics, 10:356.
diff --git a/academic/archeopteryx/References b/academic/archeopteryx/References
deleted file mode 100644
index bec0a4ddb164..000000000000
--- a/academic/archeopteryx/References
+++ /dev/null
@@ -1,4 +0,0 @@
-Please cite:
-Han M.V. and Zmasek C.M. (2009)
-phyloXML: XML for evolutionary biology and comparative genomics
-BMC Bioinformatics, 10:356.
diff --git a/academic/archeopteryx/_aptx_configuration_file.txt b/academic/archeopteryx/_aptx_configuration_file.txt
deleted file mode 100644
index a7230a42722d..000000000000
--- a/academic/archeopteryx/_aptx_configuration_file.txt
+++ /dev/null
@@ -1,502 +0,0 @@
-#  User Interface Look and Feel
-#  ----------------------------
-#  Possible values for 'native_ui'
-#    'yes' to use native (system) "look and feel"
-#    'no'  to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
-#    '?'   to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
-#          Archaeopteryx-style "look and feel" otherwise
-
-native_ui: ?
-
-
-
-#  Default Values for Options
-#  --------------------------
-#  Minimal confidence value to be displayed: 'min_confidence_value':
-#     Example: 'min_confidence_value: 50.0' (a commonly used 
-#     value for bootstrap support)
-#
-#  Font family name: 'font_family':
-#     Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
-#     It is advisable to use more than one value for font_family (in
-#     decreasing order of preference). Font family names have to be
-#     comma separated (no spaces). Spaces in font names have to be
-#     replaced by underscores (e.g. 'Arial_Unicode_MS').
-#
-#  Font size: 'font_size':
-#     Example: 'font_size: 10'
-#
-#  Screen antialias: 'antialias_screen': values: 'yes'/'no'
-#
-#  Show Scale: 'show_scale': values: 'yes'/'no'
-#
-#  Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
-#
-#  Cladogram display type: 'cladogram_type'
-#     Example: 'cladogram_type: non_lined_up'
-#     The three possible values are: lined_up
-#                                    non_lined_up
-#
-#  Default line width for PDF export: 'pdf_export_line_wdith':
-#     Example: 'pdf_export_line_width: 0.5'
-#
-#  Show overview: 'show_overview': values: 'yes'/'no'
-#
-#  Phylogeny graphics type: 'phylogeny_graphics_type':
-#     Example: 'phylogeny_graphics_type: euro_style'
-#     The eight possible values are: rectangular
-#                                    euro_style
-#                                    rounded
-#                                    curved
-#                                    triangular
-#                                    convex
-#                                    unrooted
-#                                    circular
-#
-#  Node label direction for circular and unrooted type: 'node_label_direction':
-#     Example: 'node_label_direction: horizontal'
-#     The two possible values are: horizontal
-#                                  radial
-#
-#  Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
-#
-#  Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
-#
-#  Default node shape size: 'default_node_size'
-#     Example: 'default_node_size: 6'
-#
-#  Default node shape type: 'default_node_shape'
-#     Example: 'default_node_shape: '
-#     Possible values: circle
-#                      rectangle
-#
-#  Default node shape fill: 'default_node_fill'
-#     Example: 'default_node_fill: '
-#     Possible values: solid
-#                      gradient
-#                      none
-#
-#  To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
-#     Possible values: node_name
-#                      sequence_name
-#                      gene_name
-#                      sequence_acc
-#                      sequence_mol_seq_fasta
-#                      sequence_symbol
-#                      taxonomy_scientific_name
-#                      taxonomy_code
-#                      domains
-#                      domains_collapsed
-#                      seq_annotations
-#                      go_term_ids
-#                      user_selected
-#
-#  To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
-#     Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
-#     classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
-#     Possible values: window (for output to window and buffer)
-#                      console (for output to console and buffer)
-#                      buffer_only (for output to buffer only)
-#
-#  To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
-#     Example: 'list_node_data_custom_label: Get_Node_Data'
-# 
-#  Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
-#
-#  Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
-#
-#  Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
-#
-#  Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
-#
-#  Number of fraction digits for branch length values: 'branch_length_value_digits'
-#
-#  Number of fraction digits for confidence values: 'confidence_value_digits'
-#
-#  To turn on/off background color gradient: background_gradient
-#     Example: 'background_gradient: yes'
-#
-#  To allow/not allow editing (cut, copy, and paste): allow_editing
-#     Example: 'allow_editing: yes'
-#
-#  To allow/not allow thicker strokes for very small trees: allow_thick_strokes
-#     Example: 'allow_thick_strokes: yes'
-#
-#  NH/NHX/Nexus file parsing
-#  -------------------------
-#  To replace underscores with spaces during NH/NHX/Nexus file parsing:
-#     'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
-#
-#  To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
-#  from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
-#     possible values are:
-#     'no'
-#     'pfam_strict'  (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
-#     'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
-#     'aggressive'   (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
-#
-#  Internal node labels are confidence values during NH/NHX/Nexus file parsing:
-#     'internal_labels_are_confidence_values', possible values are 'yes', 'no'
-#
-#  phyloXML parsing
-#  ----------------
-#  To ensure compatibility with all current and future 
-#  phyloXML applications and to detect malformatted and
-#  possibly erroneous data, it is strongly recommended
-#  to enable validation of all phyloXML files
-#  against the XSD Schema (see: http://www.phyloxml.org/),
-#  with:
-#  'validate_against_phyloxml_xsd_schema: true'
-
-
-min_confidence_value:                      0.0
-font_family:                               Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
-font_size:                                 10
-font_size_min:                             2
-font_size_max:                             20
-antialias_screen:                          yes
-show_scale:                                yes
-cladogram_type:                            non_lined_up
-phylogeny_graphics_type:                   rectangular
-node_label_direction:                      horizontal
-show_default_node_shapes_internal:         no
-show_default_node_shapes_external:         no
-show_node_shapes_for_nodes_with_vis_data:  yes 
-default_node_size:                         4
-default_node_shape:                        rectangle
-default_node_fill:                         solid
-pdf_export_line_width:                     0.5
-show_overview:                             yes
-overview_width:                            120
-overview_height:                           120
-overview_placement_type:                   upper_left
-color_labels_same_as_branch_length_values: no
-display_sequence_relations:                no
-show_domain_labels:                        yes
-line_up_renderable_data:                   yes
-right_align_domain_architectures:          no
-show_seq_annotation_ref_sources:           yes
-branch_length_value_digits:                3
-confidence_value_digits:                   2
-background_gradient:                       no
-allow_editing:                             yes
-allow_thick_strokes:                       no
-list_node_data_in:                         window
-list_node_data_field:                      user_selected
-list_node_data_custom_label:         
-#  NH/NHX/Nexus file parsing:
-internal_labels_are_confidence_values:     no
-replace_underscores_in_nh_parsing:         no
-taxonomy_extraction_in_nh_parsing:         no
-#  phyloXML parsing:
-validate_against_phyloxml_xsd_schema:      true
-
-
-#  Checkbox Display Selection
-#  --------------------------
-#  This is used to select which checkboxes to display
-#  and what their initial values should be.
-#  Format: 'name: display|nodisplay yes|no'
-#  Note: if an option is not displayed, it will not be enabled
-#
-#  For the following use '?' to let Archaeopteryx decide (depending on tree):
-#  - 'phylogram'
-#  - 'write_confidence_values'
-#  - 'write_events'
-
-phylogram:                      display   ?
-rollover:                       display   yes
-color_according_to_sequence:    display   no
-color_according_to_species:     display   no
-color_according_to_annotation:  display   no
-show_node_names:                display   yes
-show_seq_names:                 display   yes
-show_seq_symbols:               display   yes
-show_seq_acc:                   display   no
-show_gene_names:                display   yes
-show_taxonomy_code:             display   yes
-show_taxonomy_scientific_names: display   yes
-show_taxonomy_rank:             display   no
-show_taxonomy_common_names:     display   no
-show_taxonomy_images:           display   no
-show_annotations:               display   no
-write_confidence_values:        display   ?
-write_branch_length_values:     display   no
-write_events:                   display   ?
-use_visual_styles:              display   no
-width_branches:                 display   no
-show_domain_architectures:      display   no
-show_msa:                       display   no
-show_binary_characters:         display   no
-show_binary_character_counts:   display   no
-display_internal_data:          display   yes
-dynamically_hide_data:          display   yes
-show_relation_confidence:       display   no
-show_properties:                display   no
-show_vector_data:               display   no
-
-
-
-#  Combo-box Display Selection
-#  ---------------------------
-#  Format: 'name: display/nodisplay'
-click_to: display_node_data        display
-click_to: collapse_uncollapse      display
-click_to: uncollapse_all           display
-click_to: reroot                   display
-click_to: subtree                  display
-click_to: swap                     display
-click_to: order_subtree            display
-click_to: sort_descendants         display
-click_to: color_subtree            display
-click_to: change_node_font         display
-click_to: color_node_font          display
-click_to: open_seq_web             display
-click_to: open_pdb_web             display
-click_to: open_tax_web             display
-click_to: blast                    display
-click_to: cut_subtree              display
-click_to: copy_subtree             display
-click_to: paste_subtree            display
-click_to: delete                   display
-click_to: add_new_node             display
-click_to: edit_node_data           display
-click_to: select_nodes             display
-click_to: get_ext_descendents_data display
-
-#   Default click-to option (any of the above if set to "display")
-default_click_to: display_node_data
-
-
-
-#  Default Tree Display Colors
-#  ---------------------------
-
-display_color: background                 0x000000
-display_color: background_gradient_bottom 0x0000FF
-display_color: sequence                   0xE6E6E6
-display_color: taxonomy                   0xB4B4B4
-display_color: confidence                 0xB4B4B4
-display_color: branch_length              0x8C8C8C
-display_color: branch                     0xFFFFFF
-display_color: node_box                   0xFFFFFF
-display_color: collapsed                  0xFFFFFF
-display_color: matching_a                 0x00FF00
-display_color: matching_b                 0xFF0000
-display_color: matching_a_and_b           0xFFFF00
-display_color: duplication                0xFF0000
-display_color: speciation                 0x00FF00
-display_color: duplication_or_specation   0xFFFF00
-display_color: domain_label               0xE6E6E6
-display_color: domain_base                0x646464
-display_color: binary_domain_combinations 0x4169FF
-display_color: annotation                 0xADFF2F
-display_color: overview                   0x828282
-
-
-
-#  GUI (graphical user interface) Colors
-#  -------------------------------------
-#
-#  These are ignored if native (system) "look and feel"
-#  is being used ('native_ui: yes').
-
-gui_background_color:                 0x202020
-gui_checkbox_text_color:              0xDCDCDC
-gui_checkbox_and_button_active_color: 0xFF0000
-gui_button_text_color:                0xFFFFFF
-gui_button_background_color:          0x404040
-gui_menu_background_color:            0x000000
-gui_menu_text_color:                  0xFFFFFF
-gui_button_border_color:              0x000000
-
-
-#  Vector Data Display Colors and Sizes
-#  ------------------------------------
-vector_data_min_color:                0x0000FF
-vector_data_max_color:                0xFFFF00
-vector_data_mean_color:               0x000000
-vector_data_width:                    120
-vector_data_height:                   12
-
-
-#  Settings Specific for Archaeopteryx Applets (E and A)
-#  -----------------------------------------------------
-#  To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
-
-midpoint_reroot: yes
-
-
-
-#  Settings Specific for ArchaeopteryxE Applets
-#  --------------------------------------------
-#  To hide controls and menus: 'hide_controls_and_menus: yes'
-#  To use tabbed display     : 'use_tabbed_display: yes'
-
-hide_controls_and_menus: no
-use_tabbed_display:      yes
-
-
-
-#  Settings For Phylogenetic Inference
-#  -----------------------------------
-#  EXPERIMENTAL: DO NOT USE!!
-
-default_number_of_bootstrap_resamples: 100
-mafft_local:                            /bin/mafft
-fastme_local:                           /bin/fastme
-raxml_local:                            /bin/raxml
-
-
-
-#  Sequence colors
-#  ---------------
-#  Format: species_color: sequencename hexcolor
-sequence_color: Tubulin-alpha        0xEE0000
-sequence_color: Tubulin-beta         0x00EE00
-
-
-#  Species colors
-#  --------------
-#  Format: species_color: speciesname hexcolor
-species_color: BRAFL        0x00FFFF
-species_color: SPHGR        0x9620F0
-species_color: STRPU        0x9620F0
-species_color: CIOIN        0xFF1CAE
-species_color: CIOSA        0xFF2CAE
-species_color: BOVIN        0x5C3317
-species_color: CANFA        0x8B2323
-species_color: HUMAN        0xFF2400
-species_color: PANTR        0xCC2400
-species_color: MOUSE        0xFF7F00
-species_color: RAT          0xFFEF00
-species_color: MONDO        0xEE9A49
-species_color: ORNAN        0xCD853F
-species_color: XENLA        0x6BAA23
-species_color: XENTR        0x6BAA23
-species_color: CHICK        0xFFC125
-species_color: FUGRU        0x0000FF
-species_color: BRARE        0x0000DD
-species_color: DANRE        0x0000BB
-species_color: TETNG        0x0000AA
-species_color: ORYLA        0x000088
-species_color: GASAC        0x000066
-species_color: CAEEL        0x666699
-species_color: CAEBR        0xB0B0B0
-species_color: DROME        0x663366
-species_color: DROPS        0x996699
-species_color: APIME        0x7A7700
-species_color: AEDAE        0x8C5900
-species_color: TRICA        0x918E00
-species_color: NEMVE        0x0066CC
-species_color: HYDAT        0x3399FF
-species_color: HYDVU        0x3399FF
-species_color: LUBBA        0xF7B5CB
-species_color: GEOCY        0xF5A0BD
-species_color: AMPQE        0x009966
-species_color: SUBDO        0xC790B9
-species_color: MONBE        0xFC0FC0
-species_color: DICPU        0xFFCC33
-species_color: DICDI        0xFFCC00
-species_color: ENTHI        0x5959AB
-species_color: ARATH        0x00FF00
-species_color: POPTR        0x006400
-species_color: VITVI        0x00CD00
-species_color: GLYMA        0x00FF7F
-species_color: ORYSA        0x008B00
-species_color: ORYSJ        0x008C00
-species_color: SORBI        0x00EE76
-species_color: SELMO        0x238E23
-species_color: PHYPA        0x09F911
-species_color: OSTLU        0x7FFF00
-species_color: OSTTA        0x7FFF00
-species_color: OSTRC        0x7FFF00
-species_color: MICPU        0x66CD00
-species_color: MIC99        0x66CD00
-species_color: CHLRE        0xB3EE3A
-species_color: VOLCA        0xC0FF3E
-species_color: CHLSP        0x6B8E23
-species_color: CYAME        0xD02090
-species_color: YEAST        0xAAAAAA
-species_color: BACFR        0xFF0000
-species_color: BACTN        0xFFFF00
-species_color: MYXXD        0x0000FF
-species_color: STIAU        0x00FFFF
-species_color: BACOV        0x8C5900
-species_color: BACUN        0x66CD00
-species_color: PORGI        0x918E00
-# rank: Class
-species_color: Mammalia       0xFF0000
-species_color: mammals        0xFF0000
-# rank: Phylum
-species_color: Chordata       0x8470FF
-species_color: Echinodermata  0x6495ED
-species_color: Hemichordata   0x7EC0EE
-species_color: Arthropoda     0x7AC5CD
-species_color: Nematoda       0x7171C6
-species_color: Tardigrada     0x388E8E
-species_color: Annelida       0xC67171
-species_color: Mollusca       0x00F5FF
-species_color: Ctenophora     0xBBFFFF
-species_color: Cnidaria       0xFF83FA
-species_color: Placozoa       0xEED2EE
-species_color: Porifera       0xFF3E96
-species_color: Microsporidia  0x8B8378
-species_color: Ascomycota     0xFF6347
-species_color: Basidiomycota  0xFFD700
-species_color: Chlorophyta    0x00C78C
-species_color: Streptophyta   0x00C957
-# rank: Kingdom
-species_color: Viridiplantae  0x00FF00
-species_color: plants         0x00FF00
-species_color: Metazoa        0x0000FF
-species_color: animals        0x0000FF
-species_color: Fungi          0xFF9912
-# rank: Superkingdom
-species_color: Viruses        0xFFD700
-species_color: Bacteria       0x00FF00
-species_color: Archaea        0x0000FF
-species_color: Eukaryota      0xFF0000
-species_color: eukaryotes     0xFF0000
-
-
-
-#  Domain colors
-#  -------------
-domain_color: Cofilin_ADF     0xFC0FC0
-domain_color: TIR             0x900000
-domain_color: NACHT           0x202020
-domain_color: CARD            0xFF0000
-domain_color: Peptidase_C14   0x00FF00
-domain_color: Death           0x0000FF
-domain_color: DED             0x00FFFF
-domain_color: BIR             0xCCFF33
-domain_color: PAAD_DAPIN      0x9999CC
-domain_color: NB-ARC          0x500050
-domain_color: WD40            0x888888
-domain_color: RVT_1           0x999900
-domain_color: CBM_48          0xFF0000
-domain_color: Alpha-amylase   0x0000FF
-domain_color: Alpha-amylase_C 0x0080FF
-domain_color: CBM_48          0xFF0000
-domain_color: Alpha-amylase   0x0000FF
-domain_color: Alpha-amylase_C 0x0080FF
-domain_color: GDE_N           0x009000
-domain_color: GDE_C           0x00FF00
-domain_color: hGDE_N          0x990099
-domain_color: GDE_N_bis       0x007000
-domain_color: hGDE_central    0xFF8000
-domain_color: hGDE_amylase    0x0000EE
-domain_color: hDGE_amylase    0x0000EE
-
-
-
-#  Annotation colors
-#  -----------------
-annotation_color: dehydrogenase 0x0000FF
-annotation_color: kinase        0xFF00FF
-annotation_color: protease      0x009900
-annotation_color: transcription 0xAAAA00
-
-
-# END
diff --git a/academic/archeopteryx/archeopteryx.SlackBuild b/academic/archeopteryx/archeopteryx.SlackBuild
deleted file mode 100644
index 3f767ddbdc2c..000000000000
--- a/academic/archeopteryx/archeopteryx.SlackBuild
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/sh
-
-# Slackware build script for archeopteryx
-
-# Copyright 2014-2016 Petar Petrov slackalaxy@gmail.com
-# All rights reserved.
-#
-# Redistribution and use of this script, with or without modification, is
-# permitted provided that the following conditions are met:
-#
-# 1. Redistributions of this script must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
-#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
-#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-PRGNAM=archeopteryx
-VERSION=${VERSION:-1045}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-
-SRCNAM=forester
-ARCH=noarch
-
-CWD=$(pwd)
-TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
-OUTPUT=${OUTPUT:-/tmp}
-
-set -e
-
-rm -rf $PKG
-mkdir -p $TMP $PKG $OUTPUT
-cd $TMP
-
-install -D -m755 $CWD/${SRCNAM}_${VERSION}.jar $PKG/usr/bin/$PRGNAM.jar
-
-mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-
-# Include the example configuration file in the package. Copy it in your $HOME.
-mkdir -p $PKG/usr/share/$PRGNAM
-cp $CWD/_aptx_configuration_file.txt $PKG/usr/share/$PRGNAM
-
-# I did not find an icon, so I quickly modified some picture of an archeopteryx...
-mkdir -p $PKG/usr/share/{applications,pixmaps}
-cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
-cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
-
-mkdir -p $PKG/install
-cat $CWD/slack-desc > $PKG/install/slack-desc
-cat $CWD/doinst.sh > $PKG/install/doinst.sh
-
-cd $PKG
-/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/archeopteryx/archeopteryx.desktop b/academic/archeopteryx/archeopteryx.desktop
deleted file mode 100644
index df1f6b292948..000000000000
--- a/academic/archeopteryx/archeopteryx.desktop
+++ /dev/null
@@ -1,7 +0,0 @@
-[Desktop Entry]
-Categories=Education;
-Exec=java -Xmx2048m -jar /usr/bin/archeopteryx.jar
-Icon=archeopteryx
-Name=Archeopteryx
-StartupNotify=false
-Type=Application
diff --git a/academic/archeopteryx/archeopteryx.info b/academic/archeopteryx/archeopteryx.info
deleted file mode 100644
index 218b456e5572..000000000000
--- a/academic/archeopteryx/archeopteryx.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="archeopteryx"
-VERSION="1045"
-HOMEPAGE="https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"
-DOWNLOAD="https://dl.dropboxusercontent.com/u/14456265/forester/download/forester_1045.jar"
-MD5SUM="99b8bbb7a7763ca999a7056398637d8c"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
-REQUIRES="jdk"
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"
diff --git a/academic/archeopteryx/archeopteryx.png b/academic/archeopteryx/archeopteryx.png
deleted file mode 100644
index 5663c1b87e97..000000000000
--- a/academic/archeopteryx/archeopteryx.png
+++ /dev/null
diff --git a/academic/archeopteryx/doinst.sh b/academic/archeopteryx/doinst.sh
deleted file mode 100644
index 5fb28930db0b..000000000000
--- a/academic/archeopteryx/doinst.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-if [ -x /usr/bin/update-desktop-database ]; then
-  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
-fi
diff --git a/academic/archeopteryx/slack-desc b/academic/archeopteryx/slack-desc
deleted file mode 100644
index 84df0deffa9b..000000000000
--- a/academic/archeopteryx/slack-desc
+++ /dev/null
@@ -1,19 +0,0 @@
-# HOW TO EDIT THIS FILE:
-# The "handy ruler" below makes it easier to edit a package description.
-# Line up the first '|' above the ':' following the base package name, and
-# the '|' on the right side marks the last column you can put a character in.
-# You must make exactly 11 lines for the formatting to be correct.  It's also
-# customary to leave one space after the ':' except on otherwise blank lines.
-
-            |-----handy-ruler------------------------------------------------------|
-archeopteryx: archeopteryx (Visualise, analyse and edit phylogenetic trees)
-archeopteryx:
-archeopteryx: Archeopteryx is a software tool for the visualization, analysis,
-archeopteryx: and editing of potentially large and highly annotated phylogenetic
-archeopteryx: trees.
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx:
-archeopteryx: